WorldWideScience

Sample records for systems sophisticated molecular

  1. Sophisticated fuel handling system evolved

    International Nuclear Information System (INIS)

    Ross, D.A.

    1988-01-01

    The control systems at Sellafield fuel handling plant are described. The requirements called for built-in diagnostic features as well as the ability to handle a large sequencing application. Speed was also important; responses better than 50ms were required. The control systems are used to automate operations within each of the three main process caves - two Magnox fuel decanners and an advanced gas-cooled reactor fuel dismantler. The fuel route within the fuel handling plant is illustrated and described. ASPIC (Automated Sequence Package for Industrial Control) which was developed as a controller for the plant processes is described. (U.K.)

  2. The role of sophisticated accounting system in strategy management

    OpenAIRE

    Naranjo Gil, David

    2004-01-01

    Organizations are designing more sophisticated accounting information systems to meet the strategic goals and enhance their performance. This study examines the effect of accounting information system design on the performance of organizations pursuing different strategic priorities. The alignment between sophisticated accounting information systems and organizational strategy is analyzed. The enabling effect of the accounting information system on performance is also examined. Relationships ...

  3. STAF: A Powerful and Sophisticated CAI System.

    Science.gov (United States)

    Loach, Ken

    1982-01-01

    Describes the STAF (Science Teacher's Authoring Facility) computer-assisted instruction system developed at Leeds University (England), focusing on STAF language and major program features. Although programs for the system emphasize physical chemistry and organic spectroscopy, the system and language are general purpose and can be used in any…

  4. Sophistication and integration of plant engineering CAD-CAE systems

    International Nuclear Information System (INIS)

    Yoshinaga, Toshiaki; Hanyu, Masaharu; Ota, Yoshimi; Kobayashi, Yasuhiro.

    1995-01-01

    In respective departments in charge of basic planning, design, manufacture, inspection and construction of nuclear power plants, by the positive utilization of CAD/CAE system, efficient workings have been advanced. This time, the plant integrated CAE system wich heightens the function of these individual systems, and can make workings efficient and advanced by unifying and integrating them was developed. This system is composed of the newly developed application system and the data base system which enables the unified management of engineering data and high speed data conversion in addition to the CAD system for three-dimensional plant layout planning. On the basis of the rich experience and the proposal of improvement of designers by the application of the CAD system for three-dimensional plant layout planning to actual machines, the automation, speed increase and the visualization of input and output by graphical user interface (GUI) in the processing of respective applications were made feasible. As the advancement of plant CAE system, scenic engineering system, integrated layout CAE system, electric instrumentation design CAE system and construction planning CAE system are described. As for the integration of plant CAE systems, the integrated engineering data base, the combination of plant CAE systems, and the operation management in the dispersed environment of networks are reported. At present, Hitachi Ltd. exerts efforts for the construction of atomic energy product in formation integrated management system as the second stage of integration. (K.I.)

  5. Sophistication of burnup analysis system for fast reactor

    International Nuclear Information System (INIS)

    Yokoyama, Kenji; Hirai, Yasushi; Hyoudou, Hideaki; Tatsumi, Masahiro

    2010-02-01

    Improvement on prediction accuracy for neutronics property of fast reactor cores is one of the most important study domains in terms of both achievement of high economical plant efficiency based on reasonably advanced designs and increased reliability and safety margins. In former study, considerable improvement on prediction accuracy in neutronics design has been achieved in the development of the unified constants library as a fruit of a series of critical experiments such as JUPITER in application of the reactor constant adjustments. For design of fast reactor cores, however, improvement of not only static properties but also burnup properties is very important. For such purpose, it is necessary to improve the prediction accuracy on burnup properties using actual burnup data of 'JOYO' and 'MONJU', experimental and prototype fast reactors. Recently, study on effective burnup method for minor actinides becomes important theme. However, there is a problem that analysis work tends to become inefficient for lack of functionality suitable for analysis of composition change due to burnup since the conventional analysis system is targeted to critical assembly systems. Therefore development of burnup analysis system for fast reactors with modularity and flexibility is being done that would contribute to actual core design work and improvement of prediction accuracy. In the previous research, we have developed a prototype system which has functions of performing core and burnup calculations using given constant files (PDS files) and information based on simple and easy user input data. It has also functions of fuel shuffling which is indispensable for production systems. In the present study, we implemented functions for cell calculations and burnup calculations. With this, whole steps in analysis can be carried out with only this system. In addition, we modified the specification of user input to improve the convenience of this system. Since implementations being done so

  6. Sophistication of burnup analysis system for fast reactor (2)

    International Nuclear Information System (INIS)

    Yokoyama, Kenji; Hirai, Yasushi; Tatsumi, Masahiro

    2010-10-01

    Improvement on prediction accuracy for neutronics characteristics of fast reactor cores is one of the most important study domains in terms of both achievement of high economical plant efficiency based on reasonably advanced designs and increased reliability and safety margins. In former study, considerable improvement on prediction accuracy in neutronics design has been achieved in the development of the unified cross-section set as a fruit of a series of critical experiments such as JUPITER in application of the reactor constant adjustments. For design of fast reactor cores improvement of not only static characteristics but also burnup characteristics is very important. For such purpose, it is necessary to improve the prediction accuracy on burnup characteristics using actual burnup data of 'JOYO' and 'MONJU', experimental and prototype fast reactors. Recently, study on effective burnup method for minor actinides becomes important theme. However, there is a problem that analysis work tends to become inefficient for lack of functionality suitable for analysis of composition change due to burnup since the conventional analysis system is targeted to critical assembly systems. Therefore development of burnup analysis system for fast reactors with modularity and flexibility is being done that would contribute to actual core design work and improvement of prediction accuracy. In the previous study, we have developed a prototype system which has functions of performing core and burnup calculations using given constant files (PDS files) and information based on simple and easy user input data. It has also functions of fuel shuffling which is indispensable for power reactor analysis systems. In the present study, by extending the prototype system, features for handling of control rods and energy collapse of group constants have been designed and implemented. Computational results from the present analysis system are stored into restart files which can be accessible by

  7. Sophisticated Players and Sophisticated Agents

    NARCIS (Netherlands)

    Rustichini, A.

    1998-01-01

    A sophisticated player is an individual who takes the action of the opponents, in a strategic situation, as determined by decision of rational opponents, and acts accordingly. A sophisticated agent is rational in the choice of his action, but ignores the fact that he is part of a strategic

  8. Lexical Complexity Development from Dynamic Systems Theory Perspective: Lexical Density, Diversity, and Sophistication

    Directory of Open Access Journals (Sweden)

    Reza Kalantari

    2017-10-01

    Full Text Available This longitudinal case study explored Iranian EFL learners’ lexical complexity (LC through the lenses of Dynamic Systems Theory (DST. Fifty independent essays written by five intermediate to advanced female EFL learners in a TOEFL iBT preparation course over six months constituted the corpus of this study. Three Coh-Metrix indices (Graesser, McNamara, Louwerse, & Cai, 2004; McNamara & Graesser, 2012, three Lexical Complexity Analyzer indices (Lu, 2010, 2012; Lu & Ai, 2011, and four Vocabprofile indices (Cobb, 2000 were selected to measure different dimensions of LC. Results of repeated measures analysis of variance (RM ANOVA indicated an improvement with regard to only lexical sophistication. Positive and significant relationships were found between time and mean values in Academic Word List and Beyond-2000 as indicators of lexical sophistication. The remaining seven indices of LC, falling short of significance, tended to flatten over the course of this writing program. Correlation analyses among LC indices indicated that lexical density enjoyed positive correlations with lexical sophistication. However, lexical diversity revealed no significant correlations with both lexical density and lexical sophistication. This study suggests that DST perspective specifies a viable foundation for analyzing lexical complexity

  9. Low Level RF Including a Sophisticated Phase Control System for CTF3

    CERN Document Server

    Mourier, J; Nonglaton, J M; Syratchev, I V; Tanner, L

    2004-01-01

    CTF3 (CLIC Test Facility 3), currently under construction at CERN, is a test facility designed to demonstrate the key feasibility issues of the CLIC (Compact LInear Collider) two-beam scheme. When completed, this facility will consist of a 150 MeV linac followed by two rings for bunch-interleaving, and a test stand where 30 GHz power will be generated. In this paper, the work that has been carried out on the linac's low power RF system is described. This includes, in particular, a sophisticated phase control system for the RF pulse compressor to produce a flat-top rectangular pulse over 1.4 µs.

  10. Protecting Accelerator Control Systems in the Face of Sophisticated Cyber Attacks

    International Nuclear Information System (INIS)

    Hartman, Steven M.

    2012-01-01

    Cyber security for industrial control systems has received significant attention in the past two years. The news coverage of the Stuxnet attack, believed to be targeted at the control system for a uranium enrichment plant, brought the issue to the attention of news media and policy makers. This has led to increased scrutiny of control systems for critical infrastructure such as power generation and distribution, and industrial systems such as chemical plants and petroleum refineries. The past two years have also seen targeted network attacks aimed at corporate and government entities including US Department of Energy National Laboratories. Both of these developments have potential repercussions for the control systems of particle accelerators. The need to balance risks from potential attacks with the operational needs of an accelerator present a unique challenge for the system architecture and access model.

  11. Airbag 2000: 5th international symposium on sophisticated car occupant safety systems

    Energy Technology Data Exchange (ETDEWEB)

    Ziegahn, K F [ed.

    2000-07-01

    Modern concepts for the protection of passengers in vehicles provide the optimal degree of safety. The most well known and technically mature system is the airbag, which uses chemical gas generators, for which the dependability and service life demands are significant. All features of the system must be directly appropriate to the profile of the passenger. (AKF)

  12. Engineering FKBP-Based Destabilizing Domains to Build Sophisticated Protein Regulation Systems.

    Directory of Open Access Journals (Sweden)

    Wenlin An

    Full Text Available Targeting protein stability with small molecules has emerged as an effective tool to control protein abundance in a fast, scalable and reversible manner. The technique involves tagging a protein of interest (POI with a destabilizing domain (DD specifically controlled by a small molecule. The successful construction of such fusion proteins may, however, be limited by functional interference of the DD epitope with electrostatic interactions required for full biological function of proteins. Another drawback of this approach is the remaining endogenous protein. Here, we combined the Cre-LoxP system with an advanced DD and generated a protein regulation system in which the loss of an endogenous protein, in our case the tumor suppressor PTEN, can be coupled directly with a conditionally fine-tunable DD-PTEN. This new system will consolidate and extend the use of DD-technology to control protein function precisely in living cells and animal models.

  13. Lexical Complexity Development from Dynamic Systems Theory Perspective: Lexical Density, Diversity, and Sophistication

    OpenAIRE

    Reza Kalantari; Javad Gholami

    2017-01-01

    This longitudinal case study explored Iranian EFL learners’ lexical complexity (LC) through the lenses of Dynamic Systems Theory (DST). Fifty independent essays written by five intermediate to advanced female EFL learners in a TOEFL iBT preparation course over six months constituted the corpus of this study. Three Coh-Metrix indices (Graesser, McNamara, Louwerse, & Cai, 2004; McNamara & Graesser, 2012), three Lexical Complexity Analyzer indices (Lu, 2010, 2012; Lu & Ai, 2011...

  14. Sophisticated Calculation of the 1oo4-architecture for Safety-related Systems Conforming to IEC61508

    International Nuclear Information System (INIS)

    Hayek, A; Al Bokhaiti, M; Schwarz, M H; Boercsoek, J

    2012-01-01

    With the publication and enforcement of the standard IEC 61508 of safety related systems, recent system architectures have been presented and evaluated. Among a number of techniques and measures to the evaluation of safety integrity level (SIL) for safety-related systems, several measures such as reliability block diagrams and Markov models are used to analyze the probability of failure on demand (PFD) and mean time to failure (MTTF) which conform to IEC 61508. The current paper deals with the quantitative analysis of the novel 1oo4-architecture (one out of four) presented in recent work. Therefore sophisticated calculations for the required parameters are introduced. The provided 1oo4-architecture represents an advanced safety architecture based on on-chip redundancy, which is 3-failure safe. This means that at least one of the four channels have to work correctly in order to trigger the safety function.

  15. In Praise of the Sophists.

    Science.gov (United States)

    Gibson, Walker

    1993-01-01

    Discusses the thinking of the Greek Sophist philosophers, particularly Gorgias and Protagoras, and their importance and relevance for contemporary English instructors. Considers the problem of language as signs of reality in the context of Sophist philosophy. (HB)

  16. Sophisticating a naive Liapunov function

    International Nuclear Information System (INIS)

    Smith, D.; Lewins, J.D.

    1985-01-01

    The art of the direct method of Liapunov to determine system stability is to construct a suitable Liapunov or V function where V is to be positive definite (PD), to shrink to a center, which may be conveniently chosen as the origin, and where V is the negative definite (ND). One aid to the art is to solve an approximation to the system equations in order to provide a candidate V function. It can happen, however, that the V function is not strictly ND but vanishes at a finite number of isolated points. Naively, one anticipates that stability has been demonstrated since the trajectory of the system at such points is only momentarily tangential and immediately enters a region of inward directed trajectories. To demonstrate stability rigorously requires the construction of a sophisticated Liapunov function from what can be called the naive original choice. In this paper, the authors demonstrate the method of perturbing the naive function in the context of the well-known second-order oscillator and then apply the method to a more complicated problem based on a prompt jump model for a nuclear fission reactor

  17. Cumulative Dominance and Probabilistic Sophistication

    NARCIS (Netherlands)

    Wakker, P.P.; Sarin, R.H.

    2000-01-01

    Machina & Schmeidler (Econometrica, 60, 1992) gave preference conditions for probabilistic sophistication, i.e. decision making where uncertainty can be expressed in terms of (subjective) probabilities without commitment to expected utility maximization. This note shows that simpler and more general

  18. Synergetics of molecular systems

    CERN Document Server

    Lupichev, Lev N; Kadantsev, Vasiliy N

    2014-01-01

    Synergetics is the quantitative study of multicomponent systems that exhibit nonlinear dynamics and cooperativity. This book specifically considers basic models of the nonlinear dynamics of molecular systems and discusses relevant applications in biological physics and the polymer sciences.Emphasis is placed on specific solutions to the dynamical equations that correspond to the coherent formation of spatial-temporal structures, such as solitons, kinks and breathers, in particular. The emergence of these patterns in molecular structures provides a variety of information on their structural pro

  19. Cognitive Load and Strategic Sophistication

    OpenAIRE

    Allred, Sarah; Duffy, Sean; Smith, John

    2013-01-01

    We study the relationship between the cognitive load manipulation and strategic sophistication. The cognitive load manipulation is designed to reduce the subject's cognitive resources that are available for deliberation on a choice. In our experiment, subjects are placed under a large cognitive load (given a difficult number to remember) or a low cognitive load (given a number which is not difficult to remember). Subsequently, the subjects play a one-shot game then they are asked to recall...

  20. Molecular communications and nanonetworks from nature to practical systems

    CERN Document Server

    Atakan, Barış

    2014-01-01

    In this book, the concepts of molecular communications and nanonetworks are introduced. Throughout the book, the existing molecular communication paradigms are categorized into two main groups. The first group includes the Passive Molecular Communication (PMC) paradigms in which molecules freely diffuse to transfer information from a transmitter to a receiver. The second group includes the Active Molecular Communication (AMC) paradigms in which molecules are carried or guided by some mediators such as molecular motors, gap junction channels and bacteria. In the book, after briefly discussing why molecular communication is needed for the sophisticated nano and biotechnology applications, the existing molecular communication systems are first presented. Then, the principles of diffusion phenomena and molecular reception with absorbers and the ligand-receptor binding mechanism are introduced. Based on these principles, the communication theories and techniques are given for the PMC. Then, the physical dynamics o...

  1. Pension fund sophistication and investment policy

    NARCIS (Netherlands)

    de Dreu, J.|info:eu-repo/dai/nl/364537906; Bikker, J.A.|info:eu-repo/dai/nl/06912261X

    This paper assesses the sophistication of pension funds’ investment policies using data on 748 Dutch pension funds during the 1999–2006 period. We develop three indicators of sophistication: gross rounding of investment choices, investments in alternative sophisticated asset classes and ‘home bias’.

  2. Electrochemistry of single molecules and biomolecules, molecular scale nanostructures, and low-dimensional systems

    DEFF Research Database (Denmark)

    Nazmutdinov, Renat R.; Zinkicheva, Tamara T.; Zinkicheva, Tamara T.

    2018-01-01

    Electrochemistry at ultra-small scales, where even the single molecule or biomolecule can be characterized and manipulated, is on the way to a consolidated status. At the same time molecular electrochemistry is expanding into other areas of sophisticated nano- and molecular scale systems includin...... molecular scale metal and semiconductor nanoparticles (NPs) and other nanostructures, e.g. nanotubes, “nanoflowers” etc.. The new structures offer both new electronic properties and highly confined novel charge transfer environments....

  3. Sophisticated digestive systems in early arthropods.

    Science.gov (United States)

    Vannier, Jean; Liu, Jianni; Lerosey-Aubril, Rudy; Vinther, Jakob; Daley, Allison C

    2014-05-02

    Understanding the way in which animals diversified and radiated during their early evolutionary history remains one of the most captivating of scientific challenges. Integral to this is the 'Cambrian explosion', which records the rapid emergence of most animal phyla, and for which the triggering and accelerating factors, whether environmental or biological, are still unclear. Here we describe exceptionally well-preserved complex digestive organs in early arthropods from the early Cambrian of China and Greenland with functional similarities to certain modern crustaceans and trace these structures through the early evolutionary lineage of fossil arthropods. These digestive structures are assumed to have allowed for more efficient digestion and metabolism, promoting carnivory and macrophagy in early arthropods via predation or scavenging. This key innovation may have been of critical importance in the radiation and ecological success of Arthropoda, which has been the most diverse and abundant invertebrate phylum since the Cambrian.

  4. The value of multivariate model sophistication

    DEFF Research Database (Denmark)

    Rombouts, Jeroen; Stentoft, Lars; Violante, Francesco

    2014-01-01

    We assess the predictive accuracies of a large number of multivariate volatility models in terms of pricing options on the Dow Jones Industrial Average. We measure the value of model sophistication in terms of dollar losses by considering a set of 444 multivariate models that differ in their spec....... In addition to investigating the value of model sophistication in terms of dollar losses directly, we also use the model confidence set approach to statistically infer the set of models that delivers the best pricing performances.......We assess the predictive accuracies of a large number of multivariate volatility models in terms of pricing options on the Dow Jones Industrial Average. We measure the value of model sophistication in terms of dollar losses by considering a set of 444 multivariate models that differ...

  5. An antilock molecular braking system.

    Science.gov (United States)

    Sun, Wei-Ting; Huang, Shou-Ling; Yao, Hsuan-Hsiao; Chen, I-Chia; Lin, Ying-Chih; Yang, Jye-Shane

    2012-08-17

    A light-driven molecular brake displaying an antilock function is constructed by introducing a nonradiative photoinduced electron transfer (PET) decay channel to compete with the trans (brake-off) → cis (brake-on) photoisomerization. A fast release of the brake can be achieved by deactivating the PET process through addition of protons. The cycle of irradiation-protonation-irradiation-deprotonation conducts the brake function and mimics the antilock braking system (ABS) of vehicles.

  6. Impact of sophisticated fog spray models on accident analyses

    International Nuclear Information System (INIS)

    Roblyer, S.P.; Owzarski, P.C.

    1978-01-01

    The N-Reactor confinement system release dose to the public in a postulated accident is reduced by washing the confinement atmosphere with fog sprays. This allows a low pressure release of confinement atmosphere containing fission products through filters and out an elevated stack. The current accident analysis required revision of the CORRAL code and other codes such as CONTEMPT to properly model the N Reactor confinement into a system of multiple fog-sprayed compartments. In revising these codes, more sophisticated models for the fog sprays and iodine plateout were incorporated to remove some of the conservatism of steam condensing rate, fission product washout and iodine plateout than used in previous studies. The CORRAL code, which was used to describe the transport and deposition of airborne fission products in LWR containment systems for the Rasmussen Study, was revised to describe fog spray removal of molecular iodine (I 2 ) and particulates in multiple compartments for sprays having individual characteristics of on-off times, flow rates, fall heights, and drop sizes in changing containment atmospheres. During postulated accidents, the code determined the fission product removal rates internally rather than from input decontamination factors. A discussion is given of how the calculated plateout and washout rates vary with time throughout the analysis. The results of the accident analyses indicated that more credit could be given to fission product washout and plateout. An important finding was that the release of fission products to the atmosphere and adsorption of fission products on the filters were significantly lower than previous studies had indicated

  7. Information theory of molecular systems

    CERN Document Server

    Nalewajski, Roman F

    2006-01-01

    As well as providing a unified outlook on physics, Information Theory (IT) has numerous applications in chemistry and biology owing to its ability to provide a measure of the entropy/information contained within probability distributions and criteria of their information ""distance"" (similarity) and independence. Information Theory of Molecular Systems applies standard IT to classical problems in the theory of electronic structure and chemical reactivity. The book starts by introducing the basic concepts of modern electronic structure/reactivity theory based upon the Density Functional Theory

  8. Does underground storage still require sophisticated studies?

    International Nuclear Information System (INIS)

    Marsily, G. de

    1997-01-01

    Most countries agree to the necessity of burying high or medium-level wastes in geological layers situated at a few hundred meters below the ground level. The advantages and disadvantages of different types of rock such as salt, clay, granite and volcanic material are examined. Sophisticated studies are lead to determine the best geological confinement but questions arise about the time for which safety must be ensured. France has chosen 3 possible sites. These sites are geologically described in the article. The final place will be proposed after a testing phase of about 5 years in an underground facility. (A.C.)

  9. Systems theoretic analysis of the central dogma of molecular biology: some recent results.

    Science.gov (United States)

    Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

    2010-03-01

    This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

  10. The New Toxicology of Sophisticated Materials: Nanotoxicology and Beyond

    Science.gov (United States)

    Maynard, Andrew D.; Warheit, David B.; Philbert, Martin A.

    2011-01-01

    It has long been recognized that the physical form of materials can mediate their toxicity—the health impacts of asbestiform materials, industrial aerosols, and ambient particulate matter are prime examples. Yet over the past 20 years, toxicology research has suggested complex and previously unrecognized associations between material physicochemistry at the nanoscale and biological interactions. With the rapid rise of the field of nanotechnology and the design and production of increasingly complex nanoscale materials, it has become ever more important to understand how the physical form and chemical composition of these materials interact synergistically to determine toxicity. As a result, a new field of research has emerged—nanotoxicology. Research within this field is highlighting the importance of material physicochemical properties in how dose is understood, how materials are characterized in a manner that enables quantitative data interpretation and comparison, and how materials move within, interact with, and are transformed by biological systems. Yet many of the substances that are the focus of current nanotoxicology studies are relatively simple materials that are at the vanguard of a new era of complex materials. Over the next 50 years, there will be a need to understand the toxicology of increasingly sophisticated materials that exhibit novel, dynamic and multifaceted functionality. If the toxicology community is to meet the challenge of ensuring the safe use of this new generation of substances, it will need to move beyond “nano” toxicology and toward a new toxicology of sophisticated materials. Here, we present a brief overview of the current state of the science on the toxicology of nanoscale materials and focus on three emerging toxicology-based challenges presented by sophisticated materials that will become increasingly important over the next 50 years: identifying relevant materials for study, physicochemical characterization, and

  11. Molecular motor assembly of a biomimetic system

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Active biological molecules and functional structures can be fabricated into a bio-mimetic system by using molecular assembly method. Such materials can be used for the drug delivery, disease diagnosis and therapy, and new nanodevice construction.

  12. Does Investors' Sophistication Affect Persistence and Pricing of Discretionary Accruals?

    OpenAIRE

    Lanfeng Kao

    2007-01-01

    This paper examines whether the sophistication of market investors influences management's strategy on discretionary accounting choice, and thus changes the persistence of discretionary accruals. The results show that the persistence of discretionary accruals for firms face with naive investors is lower than that for firms face with sophisticated investors. The results also demonstrate that sophisticated investors indeed incorporate the implications of current earnings components into future ...

  13. The sophisticated control of the tram bogie on track

    Directory of Open Access Journals (Sweden)

    Radovan DOLECEK

    2015-09-01

    Full Text Available The paper deals with the problems of routing control algorithms of new conception of tram vehicle bogie. The main goal of these research activities is wear reduction of rail wheels and tracks, wear reduction of traction energy losses and increasing of running comfort. The testing experimental tram vehicle with special bogie construction powered by traction battery is utilized for these purposes. This vehicle has a rotary bogie with independent rotating wheels driven by permanent magnets synchronous motors and a solid axle. The wheel forces in bogie are measured by large amounts of the various sensors placed on the testing experimental tram vehicle. Nowadays the designed control algorithms are implemented to the vehicle superset control system. The traction requirements and track characteristics have an effect to these control algorithms. This control including sophisticated routing brings other improvements which is verified and corrected according to individual traction and driving characteristics, and opens new possibilities.

  14. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  15. Automatically Assessing Lexical Sophistication: Indices, Tools, Findings, and Application

    Science.gov (United States)

    Kyle, Kristopher; Crossley, Scott A.

    2015-01-01

    This study explores the construct of lexical sophistication and its applications for measuring second language lexical and speaking proficiency. In doing so, the study introduces the Tool for the Automatic Analysis of LExical Sophistication (TAALES), which calculates text scores for 135 classic and newly developed lexical indices related to word…

  16. The Impact of Financial Sophistication on Adjustable Rate Mortgage Ownership

    Science.gov (United States)

    Smith, Hyrum; Finke, Michael S.; Huston, Sandra J.

    2011-01-01

    The influence of a financial sophistication scale on adjustable-rate mortgage (ARM) borrowing is explored. Descriptive statistics and regression analysis using recent data from the Survey of Consumer Finances reveal that ARM borrowing is driven by both the least and most financially sophisticated households but for different reasons. Less…

  17. Probabilistic Sophistication, Second Order Stochastic Dominance, and Uncertainty Aversion

    OpenAIRE

    Simone Cerreia-Vioglio; Fabio Maccheroni; Massimo Marinacci; Luigi Montrucchio

    2010-01-01

    We study the interplay of probabilistic sophistication, second order stochastic dominance, and uncertainty aversion, three fundamental notions in choice under uncertainty. In particular, our main result, Theorem 2, characterizes uncertainty averse preferences that satisfy second order stochastic dominance, as well as uncertainty averse preferences that are probabilistically sophisticated.

  18. The First Sophists and the Uses of History.

    Science.gov (United States)

    Jarratt, Susan C.

    1987-01-01

    Reviews the history of intellectual views on the Greek sophists in three phases: (1) their disparagement by Plato and Aristotle as the morally disgraceful "other"; (2) nineteenth century British positivists' reappraisal of these relativists as ethically and scientifically superior; and (3) twentieth century versions of the sophists as…

  19. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  20. PAUL AND SOPHISTIC RHETORIC: A PERSPECTIVE ON HIS ...

    African Journals Online (AJOL)

    use of modern rhetorical theories but analyses the letter in terms of the clas- ..... If a critical reader would have had the traditional anti-sophistic arsenal ..... pressions and that 'rhetoric' is mainly a matter of communicating these thoughts.

  1. Sophistication and Performance of Italian Agri‐food Exports

    Directory of Open Access Journals (Sweden)

    Anna Carbone

    2012-06-01

    Full Text Available Nonprice competition is increasingly important in world food markets. Recently, the expression ‘export sophistication’ has been introduced in the economic literature to refer to a wide set of attributes that increase product value. An index has been proposed to measure sophistication in an indirect way through the per capita GDP of exporting countries (Lall et al., 2006; Haussmann et al., 2007.The paper applies the sophistication measure to the Italian food export sector, moving from an analysis of trends and performance of Italian food exports. An original way to disentangle different components in the temporal variation of the sophistication index is also proposed.Results show that the sophistication index offers original insights on recent trends in world food exports and with respect to Italian core food exports.

  2. Obfuscation, Learning, and the Evolution of Investor Sophistication

    OpenAIRE

    Bruce Ian Carlin; Gustavo Manso

    2011-01-01

    Investor sophistication has lagged behind the growing complexity of retail financial markets. To explore this, we develop a dynamic model to study the interaction between obfuscation and investor sophistication in mutual fund markets. Taking into account different learning mechanisms within the investor population, we characterize the optimal timing of obfuscation for financial institutions who offer retail products. We show that educational initiatives that are directed to facilitate learnin...

  3. Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

    Science.gov (United States)

    Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

    2016-03-01

    Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

  4. High sensitivity optical molecular imaging system

    Science.gov (United States)

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

    2018-02-01

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

  5. Sophisticated Communication in the Brazilian Torrent Frog Hylodes japi.

    Science.gov (United States)

    de Sá, Fábio P; Zina, Juliana; Haddad, Célio F B

    2016-01-01

    Intraspecific communication in frogs plays an important role in the recognition of conspecifics in general and of potential rivals or mates in particular and therefore with relevant consequences for pre-zygotic reproductive isolation. We investigate intraspecific communication in Hylodes japi, an endemic Brazilian torrent frog with territorial males and an elaborate courtship behavior. We describe its repertoire of acoustic signals as well as one of the most complex repertoires of visual displays known in anurans, including five new visual displays. Previously unknown in frogs, we also describe a bimodal inter-sexual communication system where the female stimulates the male to emit a courtship call. As another novelty for frogs, we show that in addition to choosing which limb to signal with, males choose which of their two vocal sacs will be used for visual signaling. We explain how and why this is accomplished. Control of inflation also provides additional evidence that vocal sac movement and color must be important for visual communication, even while producing sound. Through the current knowledge on visual signaling in Neotropical torrent frogs (i.e. hylodids), we discuss and highlight the behavioral diversity in the family Hylodidae. Our findings indicate that communication in species of Hylodes is undoubtedly more sophisticated than we expected and that visual communication in anurans is more widespread than previously thought. This is especially true in tropical regions, most likely due to the higher number of species and phylogenetic groups and/or to ecological factors, such as higher microhabitat diversity.

  6. Sophisticated Communication in the Brazilian Torrent Frog Hylodes japi.

    Directory of Open Access Journals (Sweden)

    Fábio P de Sá

    Full Text Available Intraspecific communication in frogs plays an important role in the recognition of conspecifics in general and of potential rivals or mates in particular and therefore with relevant consequences for pre-zygotic reproductive isolation. We investigate intraspecific communication in Hylodes japi, an endemic Brazilian torrent frog with territorial males and an elaborate courtship behavior. We describe its repertoire of acoustic signals as well as one of the most complex repertoires of visual displays known in anurans, including five new visual displays. Previously unknown in frogs, we also describe a bimodal inter-sexual communication system where the female stimulates the male to emit a courtship call. As another novelty for frogs, we show that in addition to choosing which limb to signal with, males choose which of their two vocal sacs will be used for visual signaling. We explain how and why this is accomplished. Control of inflation also provides additional evidence that vocal sac movement and color must be important for visual communication, even while producing sound. Through the current knowledge on visual signaling in Neotropical torrent frogs (i.e. hylodids, we discuss and highlight the behavioral diversity in the family Hylodidae. Our findings indicate that communication in species of Hylodes is undoubtedly more sophisticated than we expected and that visual communication in anurans is more widespread than previously thought. This is especially true in tropical regions, most likely due to the higher number of species and phylogenetic groups and/or to ecological factors, such as higher microhabitat diversity.

  7. Nuclear molecular structure in heavy mass systems

    International Nuclear Information System (INIS)

    Arctaedius, T.; Bargholtz, C.

    1989-04-01

    A study is made of nuclear molecular configurations involving one heavy mass partner. The stability of these configurations to mass flow and to fission is investigated as well as their population in fusion reactions. It is concluded that shell effects in combination with the effects of angular momentum may be important in stabilizing certain configurations. A possible relation of these configurations to the so called superdeformed states is pointed out. The spectrum of rotational and vibrational trasitions within molecular configurations is investigated. For sufficiently mass-asymmetric systems the engergies of vibrational transitions are comparable to the neutron separation energy. Gamma radiation from such transitions may then be observable above the background of statistical transitions. The gamma spectrum and the directional distribution of the radioation following fusion reactions with 12 C and 16 O are calculated. (authors)

  8. Molecular Simulation of Reacting Systems; TOPICAL

    International Nuclear Information System (INIS)

    THOMPSON, AIDAN P.

    2002-01-01

    The final report for a Laboratory Directed Research and Development project entitled, Molecular Simulation of Reacting Systems is presented. It describes efforts to incorporate chemical reaction events into the LAMMPS massively parallel molecular dynamics code. This was accomplished using a scheme in which several classes of reactions are allowed to occur in a probabilistic fashion at specified times during the MD simulation. Three classes of reaction were implemented: addition, chain transfer and scission. A fully parallel implementation was achieved using a checkerboarding scheme, which avoids conflicts due to reactions occurring on neighboring processors. The observed chemical evolution is independent of the number of processors used. The code was applied to two test applications: irreversible linear polymerization and thermal degradation chemistry

  9. Molecular ecology of anaerobic reactor systems

    DEFF Research Database (Denmark)

    Hofman-Bang, H. Jacob Peider; Zheng, D.; Westermann, Peter

    2003-01-01

    Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible for these ......Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible...... to the abundance of each microbe in anaerobic reactor systems by rRNA probing. This chapter focuses on various molecular techniques employed and problems encountered when elucidating the microbial ecology of anaerobic reactor systems. Methods such as quantitative dot blot/fluorescence in-situ probing using various...

  10. Financial Literacy and Financial Sophistication in the Older Population

    Science.gov (United States)

    Lusardi, Annamaria; Mitchell, Olivia S.; Curto, Vilsa

    2017-01-01

    Using a special-purpose module implemented in the Health and Retirement Study, we evaluate financial sophistication in the American population over the age of 50. We combine several financial literacy questions into an overall index to highlight which questions best capture financial sophistication and examine the sensitivity of financial literacy responses to framing effects. Results show that many older respondents are not financially sophisticated: they fail to grasp essential aspects of risk diversification, asset valuation, portfolio choice, and investment fees. Subgroups with notable deficits include women, the least educated, non-Whites, and those over age 75. In view of the fact that retirees increasingly must take on responsibility for their own retirement security, such meager levels of knowledge have potentially serious and negative implications. PMID:28553191

  11. The conceptualization and measurement of cognitive health sophistication.

    Science.gov (United States)

    Bodie, Graham D; Collins, William B; Jensen, Jakob D; Davis, Lashara A; Guntzviller, Lisa M; King, Andy J

    2013-01-01

    This article develops a conceptualization and measure of cognitive health sophistication--the complexity of an individual's conceptual knowledge about health. Study 1 provides initial validity evidence for the measure--the Healthy-Unhealthy Other Instrument--by showing its association with other cognitive health constructs indicative of higher health sophistication. Study 2 presents data from a sample of low-income adults to provide evidence that the measure does not depend heavily on health-related vocabulary or ethnicity. Results from both studies suggest that the Healthy-Unhealthy Other Instrument can be used to capture variability in the sophistication or complexity of an individual's health-related schematic structures on the basis of responses to two simple open-ended questions. Methodological advantages of the Healthy-Unhealthy Other Instrument and suggestions for future research are highlighted in the discussion.

  12. Financial Literacy and Financial Sophistication in the Older Population.

    Science.gov (United States)

    Lusardi, Annamaria; Mitchell, Olivia S; Curto, Vilsa

    2014-10-01

    Using a special-purpose module implemented in the Health and Retirement Study, we evaluate financial sophistication in the American population over the age of 50. We combine several financial literacy questions into an overall index to highlight which questions best capture financial sophistication and examine the sensitivity of financial literacy responses to framing effects. Results show that many older respondents are not financially sophisticated: they fail to grasp essential aspects of risk diversification, asset valuation, portfolio choice, and investment fees. Subgroups with notable deficits include women, the least educated, non-Whites, and those over age 75. In view of the fact that retirees increasingly must take on responsibility for their own retirement security, such meager levels of knowledge have potentially serious and negative implications.

  13. Development of a sophisticated information system including a metadatabase and regional radioecological cadastres for assessment of the radiation impact on the environment and population of the Northwest Russia and Krasnoyarsk Region

    Energy Technology Data Exchange (ETDEWEB)

    Iskra, A.A.; Burykin, A.A. [All-Russia Research Institute of Chemical Technology (Russian Federation); Lebedev, O.G.; Popov, V.K.; Churaev, R.S. [Russian Research Center Kurchatov Institute (Russian Federation)

    2004-07-01

    The goal of the 'Radinfo' project is creation of a meta-database (MDB) and radioecological cadastres, geo-referenced information systems being a basic component of those ones, and conducting (using those systems) evaluation study of possible pathways of radionuclides from the radiation-hazardous objects, radioactive waste, and contaminated areas, followed by the ranking of threats, for two priority regions of Russia selected on the basis of expert interrogation: the North-West of Russia and Krasnoyarsk region. In order to achieve the goal the following investigation tools are being created and/or applied for evaluation study on the two regions: - information data files (local databases, publications etc.) on radiation sources, radioactive waste, and contaminated areas, as well as on the environment characteristics in the studied regions; - radionuclide transfer pathways models; - sets of local geo-information systems (comprising a basic component of GIS cadastres), embracing (scanning) the areas of two regions of interest and allowing to assess the dynamics of real and probable migration of radionuclides. The RadInfo MDB development is based on use of multi-level architecture of the Web-technologies. The multi-level architecture, unlike that of conventional 'Client-Server' type, provides more versatility and scalability. In this particular case a three-level version is realized. A SQL-server (MySQL) is used as a database server. The well-known Apache Web-server is used as an application server. For its part it provides execution of scripts in the PHP language (the scripts are program extension of the server part)With such kind of configuration there is no need in using special software on the client side. Any browser (for instance, Microsoft Internet Explorer or Netscape Navigator) can be used as a workplace. The configuration is very simple as far as as its installation, adjustment and use are concerned. The meta-database and the models of

  14. Development of a sophisticated information system including a metadatabase and regional radioecological cadastres for assessment of the radiation impact on the environment and population of the Northwest Russia and Krasnoyarsk Region

    International Nuclear Information System (INIS)

    Iskra, A.A.; Burykin, A.A.; Lebedev, O.G.; Popov, V.K.; Churaev, R.S.

    2004-01-01

    The goal of the 'Radinfo' project is creation of a meta-database (MDB) and radioecological cadastres, geo-referenced information systems being a basic component of those ones, and conducting (using those systems) evaluation study of possible pathways of radionuclides from the radiation-hazardous objects, radioactive waste, and contaminated areas, followed by the ranking of threats, for two priority regions of Russia selected on the basis of expert interrogation: the North-West of Russia and Krasnoyarsk region. In order to achieve the goal the following investigation tools are being created and/or applied for evaluation study on the two regions: - information data files (local databases, publications etc.) on radiation sources, radioactive waste, and contaminated areas, as well as on the environment characteristics in the studied regions; - radionuclide transfer pathways models; - sets of local geo-information systems (comprising a basic component of GIS cadastres), embracing (scanning) the areas of two regions of interest and allowing to assess the dynamics of real and probable migration of radionuclides. The RadInfo MDB development is based on use of multi-level architecture of the Web-technologies. The multi-level architecture, unlike that of conventional 'Client-Server' type, provides more versatility and scalability. In this particular case a three-level version is realized. A SQL-server (MySQL) is used as a database server. The well-known Apache Web-server is used as an application server. For its part it provides execution of scripts in the PHP language (the scripts are program extension of the server part)With such kind of configuration there is no need in using special software on the client side. Any browser (for instance, Microsoft Internet Explorer or Netscape Navigator) can be used as a workplace. The configuration is very simple as far as as its installation, adjustment and use are concerned. The meta-database and the models of radionuclide transfer

  15. Microelectromechanical systems integrating molecular spin crossover actuators

    Energy Technology Data Exchange (ETDEWEB)

    Manrique-Juarez, Maria D. [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France); Rat, Sylvain; Salmon, Lionel; Molnár, Gábor; Bousseksou, Azzedine, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LCC, CNRS and Université de Toulouse, UPS, INP, F-31077 Toulouse (France); Mathieu, Fabrice; Saya, Daisuke; Séguy, Isabelle; Leïchlé, Thierry; Nicu, Liviu, E-mail: liviu.nicu@laas.fr, E-mail: azzedine.bousseksou@lcc-toulouse.fr [LAAS, CNRS and Université de Toulouse, INSA, UPS, F-31077 Toulouse (France)

    2016-08-08

    Silicon MEMS cantilevers coated with a 200 nm thin layer of the molecular spin crossover complex [Fe(H{sub 2}B(pz){sub 2}){sub 2}(phen)] (H{sub 2}B(pz){sub 2} = dihydrobis(pyrazolyl)borate and phen = 1,10-phenantroline) were actuated using an external magnetic field and their resonance frequency was tracked by means of integrated piezoresistive detection. The light-induced spin-state switching of the molecules from the ground low spin to the metastable high spin state at 10 K led to a well-reproducible shift of the cantilever's resonance frequency (Δf{sub r} = −0.52 Hz). Control experiments at different temperatures using coated as well as uncoated devices along with simple calculations support the assignment of this effect to the spin transition. This latter translates into changes in mechanical behavior of the cantilever due to the strong spin-state/lattice coupling. A guideline for the optimization of device parameters is proposed so as to efficiently harness molecular scale movements for large-scale mechanical work, thus paving the road for nanoelectromechanical systems (NEMS) actuators based on molecular materials.

  16. The Optical Bichromatic Force in Molecular Systems

    Science.gov (United States)

    Aldridge, Leland; Galica, Scott; Eyler, E. E.

    2015-05-01

    The optical bichromatic force has been demonstrated to be useful for slowing atomic beams much more rapidly than radiative forces. Through numerical simulations, we examine several aspects of applying the bichromatic force to molecular beams. One is the unavoidable existence of out-of-system radiative decay, requiring one or more repumping beams. We find that the average deceleration varies strongly with the repumping intensity, but when using optimal parameters, the force approaches the limiting value allowed by population statistics. Another consideration is the effect of fine and hyperfine structure. We examine a simplified multlevel model based on the B X transition in calcium monofluoride. To circumvent optical pumping into coherent dark states, we include two possible schemes: (1) a skewed dc magnetic field, and (2) rapid optical polarization switching. Our results indicate that the bichromatic force remains a viable option for creating large forces in molecular beams, with a reduction in the peak force by approximately an order of magnitude compared to a two-level atom, but little effect on the velocity range over which the force is effective. We also describe our progress towards experimental tests of the bichromatic force on a molecular beam of CaF. Supported by the National Science Foundation.

  17. Molecular marker systems for Oenothera genetics.

    Science.gov (United States)

    Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

    2008-11-01

    The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

  18. Library of sophisticated functions for analysis of nuclear spectra

    Science.gov (United States)

    Morháč, Miroslav; Matoušek, Vladislav

    2009-10-01

    In the paper we present compact library for analysis of nuclear spectra. The library consists of sophisticated functions for background elimination, smoothing, peak searching, deconvolution, and peak fitting. The functions can process one- and two-dimensional spectra. The software described in the paper comprises a number of conventional as well as newly developed methods needed to analyze experimental data. Program summaryProgram title: SpecAnalysLib 1.1 Catalogue identifier: AEDZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 42 154 No. of bytes in distributed program, including test data, etc.: 2 379 437 Distribution format: tar.gz Programming language: C++ Computer: Pentium 3 PC 2.4 GHz or higher, Borland C++ Builder v. 6. A precompiled Windows version is included in the distribution package Operating system: Windows 32 bit versions RAM: 10 MB Word size: 32 bits Classification: 17.6 Nature of problem: The demand for advanced highly effective experimental data analysis functions is enormous. The library package represents one approach to give the physicists the possibility to use the advanced routines simply by calling them from their own programs. SpecAnalysLib is a collection of functions for analysis of one- and two-parameter γ-ray spectra, but they can be used for other types of data as well. The library consists of sophisticated functions for background elimination, smoothing, peak searching, deconvolution, and peak fitting. Solution method: The algorithms of background estimation are based on Sensitive Non-linear Iterative Peak (SNIP) clipping algorithm. The smoothing algorithms are based on the convolution of the original data with several types of filters and algorithms based on discrete

  19. Finding the Fabulous Few: Why Your Program Needs Sophisticated Research.

    Science.gov (United States)

    Pfizenmaier, Emily

    1981-01-01

    Fund raising, it is argued, needs sophisticated prospect research. Professional prospect researchers play an important role in helping to identify prospective donors and also in helping to stimulate interest in gift giving. A sample of an individual work-up on a donor and a bibliography are provided. (MLW)

  20. Procles the Carthaginian: A North African Sophist in Pausanias’ Periegesis

    Directory of Open Access Journals (Sweden)

    Juan Pablo Sánchez Hernández

    2010-11-01

    Full Text Available Procles, cited by Pausanias (in the imperfect tense about a display in Rome and for an opinion about Pyrrhus of Epirus, probably was not a historian of Hellenistic date, but a contemporary sophist whom Pausanias encountered in person in Rome.

  1. SMEs and new ventures need business model sophistication

    DEFF Research Database (Denmark)

    Kesting, Peter; Günzel-Jensen, Franziska

    2015-01-01

    , and Spreadshirt, this article develops a framework that introduces five business model sophistication strategies: (1) uncover additional functions of your product, (2) identify strategic benefits for third parties, (3) take advantage of economies of scope, (4) utilize cross-selling opportunities, and (5) involve...

  2. Molecular Imaging with Activatable Reporter Systems

    Directory of Open Access Journals (Sweden)

    Gang Niu, Xiaoyuan Chen

    2012-01-01

    Full Text Available Molecular imaging is a newly emerged multiple disciplinary field that aims to visualize, characterize and quantitatively measure biological processes at cellular and molecular levels in humans and other living systems. A reporter gene is a piece of DNA encoding reporter protein, which presents as a readily measurable phenotype that can be distinguished easily from the background of endogenous protein. After being transferred into cells of organ systems (transgenes, the reporter gene can be utilized to visualize transcriptional and posttranscriptional regulation of gene expression, protein-protein interactions, or trafficking of proteins or cells in living subjects. Herein, we review previous classification of reporter genes and regroup the reporter gene based imaging as basic, inducible and activatable, based on the regulation of reporter gene transcription and post-translational modification of reporter proteins. We then focus on activatable reporters, in which the signal can be activated at the posttranslational level for visualizing protein-protein interactions, protein phosphorylation or tertiary structure changes. The applications of several types of activatable reporters will also be summarized. We conclude that activatable reporter imaging can benefit both basic biomedical research and drug development.

  3. Energy transformation in molecular electronic systems

    International Nuclear Information System (INIS)

    Kasha, M.

    1985-01-01

    Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species 1 Δ/sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on π-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs

  4. Systems Pharmacology in Small Molecular Drug Discovery

    Directory of Open Access Journals (Sweden)

    Wei Zhou

    2016-02-01

    Full Text Available Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity, target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.

  5. Development Strategies for Tourism Destinations: Tourism Sophistication vs. Resource Investments

    OpenAIRE

    Rainer Andergassen; Guido Candela

    2010-01-01

    This paper investigates the effectiveness of development strategies for tourism destinations. We argue that resource investments unambiguously increase tourism revenues and that increasing the degree of tourism sophistication, that is increasing the variety of tourism related goods and services, increases tourism activity and decreases the perceived quality of the destination's resource endowment, leading to an ambiguous effect on tourism revenues. We disentangle these two effects and charact...

  6. Computer modeling of properties of complex molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)

    2015-03-10

    Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.

  7. Strategic sophistication of individuals and teams. Experimental evidence

    Science.gov (United States)

    Sutter, Matthias; Czermak, Simon; Feri, Francesco

    2013-01-01

    Many important decisions require strategic sophistication. We examine experimentally whether teams act more strategically than individuals. We let individuals and teams make choices in simple games, and also elicit first- and second-order beliefs. We find that teams play the Nash equilibrium strategy significantly more often, and their choices are more often a best response to stated first order beliefs. Distributional preferences make equilibrium play less likely. Using a mixture model, the estimated probability to play strategically is 62% for teams, but only 40% for individuals. A model of noisy introspection reveals that teams differ from individuals in higher order beliefs. PMID:24926100

  8. Few remarks on chiral theories with sophisticated topology

    International Nuclear Information System (INIS)

    Golo, V.L.; Perelomov, A.M.

    1978-01-01

    Two classes of the two-dimensional Euclidean chiral field theoreties are singled out: 1) the field phi(x) takes the values in the compact Hermitiam symmetric space 2) the field phi(x) takes the values in an orbit of the adjoint representation of the comcompact Lie group. The theories have sophisticated topological and rich analytical structures. They are considered with the help of topological invariants (topological charges). Explicit formulae for the topological charges are indicated, and the lower bound extimate for the action is given

  9. STOCK EXCHANGE LISTING INDUCES SOPHISTICATION OF CAPITAL BUDGETING

    Directory of Open Access Journals (Sweden)

    Wesley Mendes-da-Silva

    2014-08-01

    Full Text Available This article compares capital budgeting techniques employed in listed and unlisted companies in Brazil. We surveyed the Chief Financial Officers (CFOs of 398 listed companies and 300 large unlisted companies, and based on 91 respondents, the results suggest that the CFOs of listed companies tend to use less simplistic methods more often, for example: NPV and CAPM, and that CFOs of unlisted companies are less likely to estimate the cost of equity, despite being large companies. These findings indicate that stock exchange listing may require greater sophistication of the capital budgeting process.

  10. Sophisticated Search Capabilities in the ADS Abstract Service

    Science.gov (United States)

    Eichhorn, G.; Accomazzi, A.; Grant, C. S.; Henneken, E.; Kurtz, M. J.; Murray, S. S.

    2003-12-01

    The ADS provides access to over 940,000 references from astronomy and planetary sciences publications and 1.5 million records from physics publications. It is funded by NASA and provides free access to these references, as well as to 2.4 million scanned pages from the astronomical literature. These include most of the major astronomy and several planetary sciences journals, as well as many historical observatory publications. The references now include the abstracts from all volumes of the Journal of Geophysical Research (JGR) since the beginning of 2002. We get these abstracts on a regular basis. The Kluwer journal Solar Physics has been scanned back to volume 1 and is available through the ADS. We have extracted the reference lists from this and many other journals and included them in the reference and citation database of the ADS. We have recently scanning Earth, Moon and Planets, another Kluwer journal, and will scan other Kluwer journals in the future as well. We plan on extracting references from these journals as well in the near future. The ADS has many sophisticated query features. These allow the user to formulate complex queries. Using results lists to get further information about the selected articles provide the means to quickly find important and relevant articles from the database. Three advanced feedback queries are available from the bottom of the ADS results list (in addition to regular feedback queries already available from the abstract page and from the bottom of the results list): 1. Get reference list for selected articles: This query returns all known references for the selected articles (or for all articles in the first list). The resulting list will be ranked according to how often each article is referred to and will show the most referenced articles in the field of study that created the first list. It presumably shows the most important articles in that field. 2. Get citation list for selected articles: This returns all known articles

  11. Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems.

    Science.gov (United States)

    Fujita, Takatoshi; Mochizuki, Yuji

    2018-04-19

    We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems; in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.

  12. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  13. Remote Laser Evaporative Molecular Absorption Spectroscopy Sensor System

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a sensor system capable of remotely probing the molecular composition of cold solar system targets (asteroids, comets, planets, moons), such as from a...

  14. Reaction-diffusion systems in intracellular molecular transport and control.

    Science.gov (United States)

    Soh, Siowling; Byrska, Marta; Kandere-Grzybowska, Kristiana; Grzybowski, Bartosz A

    2010-06-07

    Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.

  15. Logic circuits based on molecular spider systems.

    Science.gov (United States)

    Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

    2016-08-01

    Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  16. Musical Sophistication and the Effect of Complexity on Auditory Discrimination in Finnish Speakers

    Science.gov (United States)

    Dawson, Caitlin; Aalto, Daniel; Šimko, Juraj; Vainio, Martti; Tervaniemi, Mari

    2017-01-01

    Musical experiences and native language are both known to affect auditory processing. The present work aims to disentangle the influences of native language phonology and musicality on behavioral and subcortical sound feature processing in a population of musically diverse Finnish speakers as well as to investigate the specificity of enhancement from musical training. Finnish speakers are highly sensitive to duration cues since in Finnish, vowel and consonant duration determine word meaning. Using a correlational approach with a set of behavioral sound feature discrimination tasks, brainstem recordings, and a musical sophistication questionnaire, we find no evidence for an association between musical sophistication and more precise duration processing in Finnish speakers either in the auditory brainstem response or in behavioral tasks, but they do show an enhanced pitch discrimination compared to Finnish speakers with less musical experience and show greater duration modulation in a complex task. These results are consistent with a ceiling effect set for certain sound features which corresponds to the phonology of the native language, leaving an opportunity for music experience-based enhancement of sound features not explicitly encoded in the language (such as pitch, which is not explicitly encoded in Finnish). Finally, the pattern of duration modulation in more musically sophisticated Finnish speakers suggests integrated feature processing for greater efficiency in a real world musical situation. These results have implications for research into the specificity of plasticity in the auditory system as well as to the effects of interaction of specific language features with musical experiences. PMID:28450829

  17. Musical Sophistication and the Effect of Complexity on Auditory Discrimination in Finnish Speakers.

    Science.gov (United States)

    Dawson, Caitlin; Aalto, Daniel; Šimko, Juraj; Vainio, Martti; Tervaniemi, Mari

    2017-01-01

    Musical experiences and native language are both known to affect auditory processing. The present work aims to disentangle the influences of native language phonology and musicality on behavioral and subcortical sound feature processing in a population of musically diverse Finnish speakers as well as to investigate the specificity of enhancement from musical training. Finnish speakers are highly sensitive to duration cues since in Finnish, vowel and consonant duration determine word meaning. Using a correlational approach with a set of behavioral sound feature discrimination tasks, brainstem recordings, and a musical sophistication questionnaire, we find no evidence for an association between musical sophistication and more precise duration processing in Finnish speakers either in the auditory brainstem response or in behavioral tasks, but they do show an enhanced pitch discrimination compared to Finnish speakers with less musical experience and show greater duration modulation in a complex task. These results are consistent with a ceiling effect set for certain sound features which corresponds to the phonology of the native language, leaving an opportunity for music experience-based enhancement of sound features not explicitly encoded in the language (such as pitch, which is not explicitly encoded in Finnish). Finally, the pattern of duration modulation in more musically sophisticated Finnish speakers suggests integrated feature processing for greater efficiency in a real world musical situation. These results have implications for research into the specificity of plasticity in the auditory system as well as to the effects of interaction of specific language features with musical experiences.

  18. Advances in study of molecular imaging reporte gene systems

    International Nuclear Information System (INIS)

    Wu Tao; An Rui

    2010-01-01

    The use of molecular imaging reporter gene systems has allowed gene therapy to move from the laboratory to the clinical application, which provides methodology to monitor the expression of therapeutic gene noninvasively and achieve quantitative outcome in vivo. Recently, the radionuclide reporter gene still is the focus many studies, but MRI and optical reporter gene have gradually played a important part in reporter gene systems. On the basis of combination of multi-subject, for example applied chemistry and molecular biology, more and more new modified reporter genes and molecular probes have spread out. This paper mainly introduces the advantages and disadvantages of reporter gene system and development trends. (authors)

  19. A New Molecular Surveillance System for Leishmaniasis

    Science.gov (United States)

    Pandey, Kishor; Pandey, Basu Dev; Mallik, Arun Kumar; Acharya, Jyoti; Kato, Kentaro; Kaneko, Osamu; Ferreira, Pedro Eduardo

    2014-01-01

    Abstract. Presently, global efforts are being made to control and eradicate the deadliest tropical diseases through the improvement of adequate interventions. A critical point for programs to succeed is the prompt and accurate diagnosis in endemic regions. Rapid diagnostic tests (RDTs) are being massively deployed and used to improve diagnosis in tropical countries. In the present report, we evaluated the hypothesis of, after use for diagnosis, the reuse of the Leishmania RDT kit as a DNA source, which can be used downstream as a molecular surveillance and/or quality control tool. As a proof of principle, a polymerase chain reaction-based method was used to detect Leishmania spp. minicircle kinetoplast DNA from leishmaniasis RDT kits. Our results show that Leishmania spp. DNA can be extracted from used RDTs and may constitute an important, reliable, and affordable tool to assist in future leishmaniasis molecular surveillance methods. PMID:24752687

  20. Electron-nuclear dynamics of molecular systems

    International Nuclear Information System (INIS)

    Diz, A.; Oehrn, Y.

    1994-01-01

    The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

  1. Roman sophisticated surface modification methods to manufacture silver counterfeited coins

    Science.gov (United States)

    Ingo, G. M.; Riccucci, C.; Faraldi, F.; Pascucci, M.; Messina, E.; Fierro, G.; Di Carlo, G.

    2017-11-01

    By means of the combined use of X-ray photoelectron spectroscopy (XPS), optical microscopy (OM) and scanning electron microscopy (SEM) coupled with energy dispersive X-ray spectroscopy (EDS) the surface and subsurface chemical and metallurgical features of silver counterfeited Roman Republican coins are investigated to decipher some aspects of the manufacturing methods and to evaluate the technological ability of the Roman metallurgists to produce thin silver coatings. The results demonstrate that over 2000 ago important advances in the technology of thin layer deposition on metal substrates were attained by Romans. The ancient metallurgists produced counterfeited coins by combining sophisticated micro-plating methods and tailored surface chemical modification based on the mercury-silvering process. The results reveal that Romans were able systematically to chemically and metallurgically manipulate alloys at a micro scale to produce adherent precious metal layers with a uniform thickness up to few micrometers. The results converge to reveal that the production of forgeries was aimed firstly to save expensive metals as much as possible allowing profitable large-scale production at a lower cost. The driving forces could have been a lack of precious metals, an unexpected need to circulate coins for trade and/or a combinations of social, political and economic factors that requested a change in money supply. Finally, some information on corrosion products have been achieved useful to select materials and methods for the conservation of these important witnesses of technology and economy.

  2. DNA-Enabled Integrated Molecular Systems for Computation and Sensing

    Science.gov (United States)

    2014-05-21

    Computational devices can be chemically conjugated to different strands of DNA that are then self-assembled according to strict Watson − Crick binding rules... DNA -Enabled Integrated Molecular Systems for Computation and Sensing Craig LaBoda,† Heather Duschl,† and Chris L. Dwyer*,†,‡ †Department of...guided folding of DNA , inspired by nature, allows designs to manipulate molecular-scale processes unlike any other material system. Thus, DNA can be

  3. Estudo teórico das transições eletrônicas usando métodos simples e sofisticados Theoretical study of electronic transitions using simple and sophisticated methods

    Directory of Open Access Journals (Sweden)

    Nelson H. Morgon

    2013-01-01

    Full Text Available In this paper, the use of both simple and sophisticated models in the study of electronic transitions was explored for a set of molecular systems: C2H4, C4H4, C4H6, C6H6, C6H8, "C8", C60, and [H2NCHCH(CHCHkCHNH2]+, where k = 0 to 4. The simple model of the free particle (1D, 2D, and 3D boxes, rings or spherical surfaces, considering the boundary conditions, was found to yield similar results to the sophisticated theoretical methods such as EOM-CCSD/6-311++G** or TD(NStates=5,Root=1-M06-2X/6-311++G**.

  4. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

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

  5. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    International Nuclear Information System (INIS)

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

    2002-01-01

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

  6. RSYST: From nuclear reactor calculations towards a highly sophisticated scientific software integration environment

    International Nuclear Information System (INIS)

    Noack, M.; Seybold, J.; Ruehle, R.

    1996-01-01

    The software environment RSYST was originally used to solve problems of reactor physics. The consideration of advanced scientific simulation requirements and the strict application of modern software design principles led to a system which is perfectly suitable to solve problems in various complex scientific problem domains. Starting with a review of the early days of RSYST, we describe the straight evolution driven by the need of software environment which combines the advantages of a high-performance database system with the capability to integrate sophisticated scientific technical applications. The RSYST architecture is presented and the data modelling capabilities are described. To demonstrate the powerful possibilities and flexibility of the RSYST environment, we describe a wide range of RSYST applications, e.g., mechanical simulations of multibody systems, which are used in biomechanical research, civil engineering and robotics. In addition, a hypermedia system which is used for scientific technical training and documentation is presented. (orig.) [de

  7. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  8. Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.

    Science.gov (United States)

    Okaty, Benjamin W; Freret, Morgan E; Rood, Benjamin D; Brust, Rachael D; Hennessy, Morgan L; deBairos, Danielle; Kim, Jun Chul; Cook, Melloni N; Dymecki, Susan M

    2015-11-18

    Serotonergic (5HT) neurons modulate diverse behaviors and physiology and are implicated in distinct clinical disorders. Corresponding diversity in 5HT neuronal phenotypes is becoming apparent and is likely rooted in molecular differences, yet a comprehensive approach characterizing molecular variation across the 5HT system is lacking, as is concomitant linkage to cellular phenotypes. Here we combine intersectional fate mapping, neuron sorting, and genome-wide RNA-seq to deconstruct the mouse 5HT system at multiple levels of granularity-from anatomy, to genetic sublineages, to single neurons. Our unbiased analyses reveal principles underlying system organization, 5HT neuron subtypes, constellations of differentially expressed genes distinguishing subtypes, and predictions of subtype-specific functions. Using electrophysiology, subtype-specific neuron silencing, and conditional gene knockout, we show that these molecularly defined 5HT neuron subtypes are functionally distinct. Collectively, this resource classifies molecular diversity across the 5HT system and discovers sertonergic subtypes, markers, organizing principles, and subtype-specific functions with potential disease relevance. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    Science.gov (United States)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  10. Particle tracking in sophisticated CAD models for simulation purposes

    International Nuclear Information System (INIS)

    Sulkimo, J.; Vuoskoski, J.

    1995-01-01

    The transfer of physics detector models from computer aided design systems to physics simulation packages like GEANT suffers from certain limitations. In addition, GEANT is not able to perform particle tracking in CAD models. We describe an application which is able to perform particle tracking in boundary models constructed in CAD systems. The transfer file format used is the new international standard, STEP. The design and implementation of the application was carried out using object-oriented techniques. It will be integrated in the future object-oriented version of GEANT. (orig.)

  11. Particle tracking in sophisticated CAD models for simulation purposes

    Science.gov (United States)

    Sulkimo, J.; Vuoskoski, J.

    1996-02-01

    The transfer of physics detector models from computer aided design systems to physics simulation packages like GEANT suffers from certain limitations. In addition, GEANT is not able to perform particle tracking in CAD models. We describe an application which is able to perform particle tracking in boundary models constructed in CAD systems. The transfer file format used is the new international standard, STEP. The design and implementation of the application was carried out using object-oriented techniques. It will be integrated in the future object-oriented version of GEANT.

  12. Molecular biophysics: detection and characterization of damage in molecular, cellular, and physiological systems

    International Nuclear Information System (INIS)

    Danyluk, S.S.

    1979-01-01

    This section contains summaries of research on the detection and characterization of damage in molecular, cellular, and physiological systems. Projects under investigation in this section include: chemical synthesis of nucleic acid derivatives; structural and conformational properties of biological molecules in solution; crystallographic and chemical studies of immunoglobulin structure; instrument design and development for x-ray and neutron scattering studies of biological molecules; and chromobiology and circadian regulation

  13. Sophisticated visualization algorithms for analysis of multidimensional experimental nuclear spectra

    International Nuclear Information System (INIS)

    Morhac, M.; Kliman, J.; Matousek, V.; Turzo, I.

    2004-01-01

    This paper describes graphical models of visualization of 2-, 3-, 4-dimensional scalar data used in nuclear data acquisition, processing and visualization system developed at the Institute of Physics, Slovak Academy of Sciences. It focuses on presentation of nuclear spectra (histograms). However it can be successfully applied for visualization of arrays of other data types. In the paper we present conventional as well as new developed surface and volume rendering visualization techniques used (Authors)

  14. Present status and future of the sophisticated work station

    Science.gov (United States)

    Ishida, Haruhisa

    The excellency of the work station is explained, by comparing the functions of software and hardware of work station with those of personal computer. As one of the examples utilizing the functions of work station, desk top publishing is explained. By describing the competition between the Group of ATT · Sun Microsystems which intends to have the leadership by integrating Berkeley version which is most popular at this moment and System V version, and the group led by IBM, future of UNIX as OS of work station is predicted. Development of RISC processor, TRON Plan and Sigma Projects by MITI are also mentioned as its background.

  15. A sophisticated programmable miniaturised pump for insulin delivery.

    Science.gov (United States)

    Klein, J C; Slama, G

    1980-09-01

    We have conceived a truly pre-programmable infusion system usable for intravenous administration of insulin in diabetic subjects. The original system has been built into a small, commercially available, syringe-pump of which only the case and the mechanical parts have been kept. The computing until has a timer, a programmable memory of 512 words by 8 bits and a digital-to-frequency converter to run the motor which drives the syringe. The memory contains 8 profiles of insulin injections stored in digital form over 64 words. Each profile is selected by the patient before eating according to the carbohydrate content of the planned meal and last about two hours, starting from and returning to the basal rate of insulin, at which it remains until next profile selection. Amount, profiles and duration of insulin injection are either mean values deduced from previous studies with a closed-loop artificial pancreas or personally fitted values; they are stored in an instantly replaceable memory cell. This device allows the patient to choose the time, nature and amount of his food intake.

  16. Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

    Science.gov (United States)

    Saenz, A.

    2008-07-01

    The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some

  17. Lexical Sophistication as a Multidimensional Phenomenon: Relations to Second Language Lexical Proficiency, Development, and Writing Quality

    Science.gov (United States)

    Kim, Minkyung; Crossley, Scott A.; Kyle, Kristopher

    2018-01-01

    This study conceptualizes lexical sophistication as a multidimensional phenomenon by reducing numerous lexical features of lexical sophistication into 12 aggregated components (i.e., dimensions) via a principal component analysis approach. These components were then used to predict second language (L2) writing proficiency levels, holistic lexical…

  18. The predictors of economic sophistication: media, interpersonal communication and negative economic experiences

    NARCIS (Netherlands)

    Kalogeropoulos, A.; Albæk, E.; de Vreese, C.H.; van Dalen, A.

    2015-01-01

    In analogy to political sophistication, it is imperative that citizens have a certain level of economic sophistication, especially in times of heated debates about the economy. This study examines the impact of different influences (media, interpersonal communication and personal experiences) on

  19. Isocratean Discourse Theory and Neo-Sophistic Pedagogy: Implications for the Composition Classroom.

    Science.gov (United States)

    Blair, Kristine L.

    With the recent interest in the fifth century B.C. theories of Protagoras and Gorgias come assumptions about the philosophical affinity of the Greek educator Isocrates to this pair of older sophists. Isocratean education in discourse, with its emphasis on collaborative political discourse, falls within recent definitions of a sophist curriculum.…

  20. Aristotle and Social-Epistemic Rhetoric: The Systematizing of the Sophistic Legacy.

    Science.gov (United States)

    Allen, James E.

    While Aristotle's philosophical views are more foundational than those of many of the Older Sophists, Aristotle's rhetorical theories inherit and incorporate many of the central tenets ascribed to Sophistic rhetoric, albeit in a more systematic fashion, as represented in the "Rhetoric." However, Aristotle was more than just a rhetorical…

  1. Modern devices the simple physics of sophisticated technology

    CERN Document Server

    Joseph, Charles L

    2016-01-01

    This book discusses the principles of physics through applications of state-of-the-art technologies and advanced instruments. The authors use diagrams, sketches, and graphs coupled with equations and mathematical analysis to enhance the reader's understanding of modern devices. Readers will learn to identify common underlying physical principles that govern several types of devices, while gaining an understanding of the performance trade-off imposed by the physical limitations of various processing methods. The topics discussed in the book assume readers have taken an introductory physics course, college algebra, and have a basic understanding of calculus. * Describes the basic physics behind a large number of devices encountered in everyday life, from the air conditioner to Blu-ray discs * Covers state-of-the-art devices such as spectrographs, photoelectric image sensors, spacecraft systems, astronomical and planetary observatories, biomedical imaging instruments, particle accelerators, and jet engines * Inc...

  2. Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems.

    Science.gov (United States)

    Dresselhaus, Thomas; Yang, Jack; Kumbhar, Sadhana; Waller, Mark P

    2013-04-09

    Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

  3. Molecular mechanisms of aging and immune system regulation in Drosophila.

    Science.gov (United States)

    Eleftherianos, Ioannis; Castillo, Julio Cesar

    2012-01-01

    Aging is a complex process that involves the accumulation of deleterious changes resulting in overall decline in several vital functions, leading to the progressive deterioration in physiological condition of the organism and eventually causing disease and death. The immune system is the most important host-defense mechanism in humans and is also highly conserved in insects. Extensive research in vertebrates has concluded that aging of the immune function results in increased susceptibility to infectious disease and chronic inflammation. Over the years, interest has grown in studying the molecular interaction between aging and the immune response to pathogenic infections. The fruit fly Drosophila melanogaster is an excellent model system for dissecting the genetic and genomic basis of important biological processes, such as aging and the innate immune system, and deciphering parallel mechanisms in vertebrate animals. Here, we review the recent advances in the identification of key players modulating the relationship between molecular aging networks and immune signal transduction pathways in the fly. Understanding the details of the molecular events involved in aging and immune system regulation will potentially lead to the development of strategies for decreasing the impact of age-related diseases, thus improving human health and life span.

  4. Selective excitation, relaxation, and energy channeling in molecular systems

    International Nuclear Information System (INIS)

    Rhodes, W.C.

    1993-08-01

    Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems

  5. Assembly, destruction and manipulation of atomic, molecular and complex systems

    International Nuclear Information System (INIS)

    Le Padellec, Arnaud Pierre Frederic

    2003-04-01

    In this report for Accreditation to Supervise Researches (HDR), the author first indicates his professional curriculum (diplomas, teaching activities, responsibilities in the field of education and research, publications), and then proposes a presentation of his scientific works and researches. He notably proposes an overview of the different experimental techniques he implemented: CRYRING storage ring, confluent beams, flow post-discharge with mass spectrometry and Langmuir probe, crossed beams, and so on. He reports works dealing with the manipulation and destruction of atomic, molecular and complex systems: detachment of atomic anions by electronic impact, detachment and dissociation of small carbon aggregates by electronic impact, dissociative recombination, dissociative ionisation and excitation, creation of pairs of ions, manipulation of sodium fluoride aggregates. He finally presents research projects regarding the assembly of molecular and complex systems

  6. Hi-tech in space - Rosetta - a space sophisticate

    Science.gov (United States)

    2004-02-01

    The European Space Agency’s Rosetta mission will be getting under way in February 2004. The Rosetta spacecraft will be pairing up with Comet 67P/Churyumov-Gerasimenko and accompanying it on its journey, investigating the comet’s composition and the dynamic processes at work as it flies sunwards. The spacecraft will even deposit a lander on the comet. “This will be our first direct contact with the surface of a comet,” said Dr Manfred Warhaut, Operations Manager for the Rosetta mission at ESA's European Space Operations Centre (ESOC) in Darmstadt, Germany. The trip is certainly not short: Rosetta will need ten years just to reach the comet. This places extreme demands on its hardware; when the probe meets up with the comet, all instruments must be fully operational, especially since it will have been in “hibernation” for 2 and a half years of its journey. During this ‘big sleep’, all systems, scientific instruments included, are turned off. Only the on-board computer remains active. Twelve cubic metres of technical wizardry Rosetta’s hardware fits into a sort of aluminium box measuring just 12 cubic metres. The scientific payload is mounted in the upper part, while the subsystems - on-board computer, transmitter and propulsion system - are housed below. The lander is fixed to the opposite side of the probe from the steerable antenna. As the spacecraft orbits the comet, the scientific instruments will at all times be pointed towards its surface; the antenna and solar panels will point towards the Earth and Sun respectively. For trajectory and attitude control and for the major braking manœuvres, Rosetta is equipped with 24 thrusters each delivering 10 N. That corresponds to the force needed here on Earth to hold a bag containing 10 apples. Rosetta sets off with 1650 kg of propellant on board, accounting for more than half its mass at lift-off. Just 20% of total mass is available for scientific purposes. So when developing the research instruments

  7. Interactive display of molecular models using a microcomputer system

    Science.gov (United States)

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

    1980-01-01

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

  8. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  9. Review and application of group theory to molecular systems biology.

    Science.gov (United States)

    Rietman, Edward A; Karp, Robert L; Tuszynski, Jack A

    2011-06-22

    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.

  10. Olfactory memory formation in Drosophila: from molecular to systems neuroscience.

    Science.gov (United States)

    Davis, Ronald L

    2005-01-01

    The olfactory nervous system of insects and mammals exhibits many similarities, which suggests that the mechanisms for olfactory learning may be shared. Molecular genetic investigations of Drosophila learning have uncovered numerous genes whose gene products are essential for olfactory memory formation. Recent studies of the products of these genes have continued to expand the range of molecular processes known to underlie memory formation. Recent research has also broadened the neuroanatomical areas thought to mediate olfactory learning to include the antennal lobes in addition to a previously accepted and central role for the mushroom bodies. The roles for neurons extrinsic to the mushroom body neurons are becoming better defined. Finally, the genes identified to participate in Drosophila olfactory learning have conserved roles in mammalian organisms, highlighting the value of Drosophila for gene discovery.

  11. Nucleocytoplasmic Transport: A Paradigm for Molecular Logistics in Artificial Systems.

    Science.gov (United States)

    Vujica, Suncica; Zelmer, Christina; Panatala, Radhakrishnan; Lim, Roderick Y H

    2016-01-01

    Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes, polymersomes or hybrid lipo-polymersomes that display different membrane-spanning channels and/or enclose molecular modules. To achieve more complex functionality, an artificial organelle should ideally sustain a continuous influx of essential macromolecular modules (i.e. cargoes) and metabolites against an outflow of reaction products. This would benefit from the incorporation of selective nanopores as well as specific trafficking factors that facilitate cargo selectivity, translocation efficiency, and directionality. Towards this goal, we describe how proteinaceous cargoes are transported between the nucleus and cytoplasm by nuclear pore complexes and the biological trafficking machinery in living cells (i.e. nucleocytoplasmic transport). On this basis, we discuss how biomimetic control may be implemented to selectively import, compartmentalize and accumulate diverse macromolecular modules against concentration gradients in artificial organelles.

  12. A new parallel molecular dynamics algorithm for organic systems

    International Nuclear Information System (INIS)

    Plimpton, S.; Hendrickson, B.; Heffelfinger, G.

    1993-01-01

    A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed

  13. DNA barcode-based molecular identification system for fish species.

    Science.gov (United States)

    Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

    2010-12-01

    In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

  14. DCMS: A data analytics and management system for molecular simulation.

    Science.gov (United States)

    Kumar, Anand; Grupcev, Vladimir; Berrada, Meryem; Fogarty, Joseph C; Tu, Yi-Cheng; Zhu, Xingquan; Pandit, Sagar A; Xia, Yuni

    Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface ( i.e. , SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.

  15. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  16. Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

    Science.gov (United States)

    Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

    2015-12-01

    Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models

  17. The tool for the automatic analysis of lexical sophistication (TAALES): version 2.0.

    Science.gov (United States)

    Kyle, Kristopher; Crossley, Scott; Berger, Cynthia

    2017-07-11

    This study introduces the second release of the Tool for the Automatic Analysis of Lexical Sophistication (TAALES 2.0), a freely available and easy-to-use text analysis tool. TAALES 2.0 is housed on a user's hard drive (allowing for secure data processing) and is available on most operating systems (Windows, Mac, and Linux). TAALES 2.0 adds 316 indices to the original tool. These indices are related to word frequency, word range, n-gram frequency, n-gram range, n-gram strength of association, contextual distinctiveness, word recognition norms, semantic network, and word neighbors. In this study, we validated TAALES 2.0 by investigating whether its indices could be used to model both holistic scores of lexical proficiency in free writes and word choice scores in narrative essays. The results indicated that the TAALES 2.0 indices could be used to explain 58% of the variance in lexical proficiency scores and 32% of the variance in word-choice scores. Newly added TAALES 2.0 indices, including those related to n-gram association strength, word neighborhood, and word recognition norms, featured heavily in these predictor models, suggesting that TAALES 2.0 represents a substantial upgrade.

  18. Electronic structure, transport, and collective effects in molecular layered systems

    Directory of Open Access Journals (Sweden)

    Torsten Hahn

    2017-10-01

    Full Text Available The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc and a flourinated copper phthalocyanine–manganese phthalocyanine (F16CoPc/MnPc heterostructure, are investigated by means of density functional theory (DFT and the non-equilibrium Green’s function (NEGF approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

  19. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

  20. Intermolecular thermoelectric-like effects in molecular nano electronic systems

    International Nuclear Information System (INIS)

    Sabzyan, H.; Safari, R.

    2012-01-01

    Intramolecular thermoelectric-like coefficients are introduced and computed of a single molecule nano electronic system. Values of the electronic Intramolecular thermoelectric-like coefficients are calculated based on the density and energy transfers between different parts of the molecule using quantum theory of atoms in molecule. Since, Joule and Peltier heating are even (symmetrical) and odd (antisymmetric) functions of the external bias, it is possible to divide Intramolecular thermoelectric-like coefficients into two components, symmetrical and antisymmetrical Intramolecular thermoelectric-like coefficients, which describe the intramolecular Joule-like and Peltier-like effects, respectively. In addition, a semiclassical temperature model is presented to describe intramolecular temperature mapping (intramolecular energy distributions) in molecular nano electronic systems.

  1. Encounters of The Solar System With Molecular Clouds

    International Nuclear Information System (INIS)

    Wickramasinghe, J. T.

    2008-01-01

    The solar system has penetrated about 5 -- 10 giant molecular clouds over its history, and passes within 5 parsecs of a star-forming nebula every 100 million years or so. Numerical simulations of the effect of such encounters in perturbing the Oort cloud of comets are carried out using standard n-body computational techniques. It is found that the ingress of comets into the inner planetary system during such encounters amounts to factors of ∼100 over the average. During an encounter the impact rate of comets onto Earth increases by a comparable factor. The of ages of impact craters on the Earth is shown to be consistent with predictions from the model

  2. The musicality of non-musicians: an index for assessing musical sophistication in the general population.

    Directory of Open Access Journals (Sweden)

    Daniel Müllensiefen

    Full Text Available Musical skills and expertise vary greatly in Western societies. Individuals can differ in their repertoire of musical behaviours as well as in the level of skill they display for any single musical behaviour. The types of musical behaviours we refer to here are broad, ranging from performance on an instrument and listening expertise, to the ability to employ music in functional settings or to communicate about music. In this paper, we first describe the concept of 'musical sophistication' which can be used to describe the multi-faceted nature of musical expertise. Next, we develop a novel measurement instrument, the Goldsmiths Musical Sophistication Index (Gold-MSI to assess self-reported musical skills and behaviours on multiple dimensions in the general population using a large Internet sample (n = 147,636. Thirdly, we report results from several lab studies, demonstrating that the Gold-MSI possesses good psychometric properties, and that self-reported musical sophistication is associated with performance on two listening tasks. Finally, we identify occupation, occupational status, age, gender, and wealth as the main socio-demographic factors associated with musical sophistication. Results are discussed in terms of theoretical accounts of implicit and statistical music learning and with regard to social conditions of sophisticated musical engagement.

  3. Moral foundations and political attitudes: The moderating role of political sophistication.

    Science.gov (United States)

    Milesi, Patrizia

    2016-08-01

    Political attitudes can be associated with moral concerns. This research investigated whether people's level of political sophistication moderates this association. Based on the Moral Foundations Theory, this article examined whether political sophistication moderates the extent to which reliance on moral foundations, as categories of moral concerns, predicts judgements about policy positions. With this aim, two studies examined four policy positions shown by previous research to be best predicted by the endorsement of Sanctity, that is, the category of moral concerns focused on the preservation of physical and spiritual purity. The results showed that reliance on Sanctity predicted political sophisticates' judgements, as opposed to those of unsophisticates, on policy positions dealing with equal rights for same-sex and unmarried couples and with euthanasia. Political sophistication also interacted with Fairness endorsement, which includes moral concerns for equal treatment of everybody and reciprocity, in predicting judgements about equal rights for unmarried couples, and interacted with reliance on Authority, which includes moral concerns for obedience and respect for traditional authorities, in predicting opposition to stem cell research. Those findings suggest that, at least for these particular issues, endorsement of moral foundations can be associated with political attitudes more strongly among sophisticates than unsophisticates. © 2015 International Union of Psychological Science.

  4. Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species.

    Directory of Open Access Journals (Sweden)

    Marie Devaine

    2017-11-01

    Full Text Available Theory of Mind (ToM, i.e. the ability to understand others' mental states, endows humans with highly adaptive social skills such as teaching or deceiving. Candidate evolutionary explanations have been proposed for the unique sophistication of human ToM among primates. For example, the Machiavellian intelligence hypothesis states that the increasing complexity of social networks may have induced a demand for sophisticated ToM. This type of scenario ignores neurocognitive constraints that may eventually be crucial limiting factors for ToM evolution. In contradistinction, the cognitive scaffolding hypothesis asserts that a species' opportunity to develop sophisticated ToM is mostly determined by its general cognitive capacity (on which ToM is scaffolded. However, the actual relationships between ToM sophistication and either brain volume (a proxy for general cognitive capacity or social group size (a proxy for social network complexity are unclear. Here, we let 39 individuals sampled from seven non-human primate species (lemurs, macaques, mangabeys, orangutans, gorillas and chimpanzees engage in simple dyadic games against artificial ToM players (via a familiar human caregiver. Using computational analyses of primates' choice sequences, we found that the probability of exhibiting a ToM-compatible learning style is mainly driven by species' brain volume (rather than by social group size. Moreover, primates' social cognitive sophistication culminates in a precursor form of ToM, which still falls short of human fully-developed ToM abilities.

  5. The musicality of non-musicians: an index for assessing musical sophistication in the general population.

    Science.gov (United States)

    Müllensiefen, Daniel; Gingras, Bruno; Musil, Jason; Stewart, Lauren

    2014-01-01

    Musical skills and expertise vary greatly in Western societies. Individuals can differ in their repertoire of musical behaviours as well as in the level of skill they display for any single musical behaviour. The types of musical behaviours we refer to here are broad, ranging from performance on an instrument and listening expertise, to the ability to employ music in functional settings or to communicate about music. In this paper, we first describe the concept of 'musical sophistication' which can be used to describe the multi-faceted nature of musical expertise. Next, we develop a novel measurement instrument, the Goldsmiths Musical Sophistication Index (Gold-MSI) to assess self-reported musical skills and behaviours on multiple dimensions in the general population using a large Internet sample (n = 147,636). Thirdly, we report results from several lab studies, demonstrating that the Gold-MSI possesses good psychometric properties, and that self-reported musical sophistication is associated with performance on two listening tasks. Finally, we identify occupation, occupational status, age, gender, and wealth as the main socio-demographic factors associated with musical sophistication. Results are discussed in terms of theoretical accounts of implicit and statistical music learning and with regard to social conditions of sophisticated musical engagement.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  7. Charge migration and charge transfer in molecular systems

    Directory of Open Access Journals (Sweden)

    Hans Jakob Wörner

    2017-11-01

    Full Text Available The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer. This review covers recent research that addresses the following questions. Can we reconstruct the migration of charge across a molecule on the atomic length and electronic time scales? Can we use strong laser fields to control charge migration? Can we temporally resolve and understand intramolecular charge transfer in dissociative ionization of small molecules, in transition-metal complexes and in conjugated polymers? Can we tailor molecular systems towards specific charge-transfer processes? What are the time scales of the elementary steps of charge transfer in liquids and nanoparticles? Important new insights into each of these topics, obtained from state-of-the-art ultrafast spectroscopy and/or theoretical methods, are summarized in this review.

  8. Evidence for systems-level molecular mechanisms of tumorigenesis

    Directory of Open Access Journals (Sweden)

    Capellá Gabriel

    2007-06-01

    Full Text Available Abstract Background Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. Results Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs" defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree and global (betweenness and closeness measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. Conclusion Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.

  9. Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

    Science.gov (United States)

    Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

    2018-04-01

    Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.

  10. Molecular dynamic simulations of the sputtering of multilayer organic systems

    CERN Document Server

    Postawa, Z; Piaskowy, J; Krantzman, K; Winograd, N; Garrison, B J

    2003-01-01

    Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag left brace 1 1 1 right brace surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.

  11. Pancreatic Cancer Gene Therapy: From Molecular Targets to Delivery Systems

    Energy Technology Data Exchange (ETDEWEB)

    Fillat, Cristina, E-mail: cristina.fillat@crg.es; Jose, Anabel; Ros, Xavier Bofill-De; Mato-Berciano, Ana; Maliandi, Maria Victoria; Sobrevals, Luciano [Programa Gens i Malaltia, Centre de Regulació Genòmica-CRG, UPF, Parc de Recerca Biomedica de Barcelona-PRBB and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona (Spain)

    2011-01-18

    The continuous identification of molecular changes deregulating critical pathways in pancreatic tumor cells provides us with a large number of novel candidates to engineer gene-targeted approaches for pancreatic cancer treatment. Targets—both protein coding and non-coding—are being exploited in gene therapy to influence the deregulated pathways to facilitate cytotoxicity, enhance the immune response or sensitize to current treatments. Delivery vehicles based on viral or non-viral systems as well as cellular vectors with tumor homing characteristics are a critical part of the design of gene therapy strategies. The different behavior of tumoral versus non-tumoral cells inspires vector engineering with the generation of tumor selective products that can prevent potential toxic-associated effects. In the current review, a detailed analysis of the different targets, the delivery vectors, the preclinical approaches and a descriptive update on the conducted clinical trials are presented. Moreover, future possibilities in pancreatic cancer treatment by gene therapy strategies are discussed.

  12. Isolating strong-field dynamics in molecular systems

    Science.gov (United States)

    Orenstein, Gal; Pedatzur, Oren; Uzan, Ayelet J.; Bruner, Barry D.; Mairesse, Yann; Dudovich, Nirit

    2017-05-01

    Strong-field ionization followed by recollision provides a unique pump-probe measurement which reveals a range of electronic processes, combining sub-Angstrom spatial and attosecond temporal resolution. A major limitation of this approach is imposed by the coupling between the spatial and temporal degrees of freedom. In this paper we focus on the study of high harmonic generation and demonstrate the ability to isolate the internal dynamics—decoupling the temporal information from the spatial one. By applying an in situ approach we reveal the universality of the intrinsic pump-probe measurement and establish its validity in molecular systems. When several orbitals are involved we identify the fingerprint of the transition from the single-channel case into the multiple-channel dynamics, where complex multielectron phenomena are expected to be observed.

  13. Differential ethnic associations between maternal flexibility and play sophistication in toddlers born very low birth weight

    Science.gov (United States)

    Erickson, Sarah J.; Montague, Erica Q.; Maclean, Peggy C.; Bancroft, Mary E.; Lowe, Jean R.

    2013-01-01

    Children born very low birth weight (development of self-regulation and effective functional skills, and play serves as an important avenue of early intervention. The current study investigated associations between maternal flexibility and toddler play sophistication in Caucasian, Spanish speaking Hispanic, English speaking Hispanic, and Native American toddlers (18-22 months adjusted age) in a cross-sectional cohort of 73 toddlers born VLBW and their mothers. We found that the association between maternal flexibility and toddler play sophistication differed by ethnicity (F(3,65) = 3.34, p = .02). In particular, Spanish speaking Hispanic dyads evidenced a significant positive association between maternal flexibility and play sophistication of medium effect size. Results for Native Americans were parallel to those of Spanish speaking Hispanic dyads: the relationship between flexibility and play sophistication was positive and of small-medium effect size. Findings indicate that for Caucasians and English speaking Hispanics, flexibility evidenced a non-significant (negative and small effect size) association with toddler play sophistication. Significant follow-up contrasts revealed that the associations for Caucasian and English speaking Hispanic dyads were significantly different from those of the other two ethnic groups. Results remained unchanged after adjusting for the amount of maternal language, an index of maternal engagement and stimulation; and after adjusting for birth weight, gestational age, gender, test age, cognitive ability, as well maternal age, education, and income. Our results provide preliminary evidence that ethnicity and acculturation may mediate the association between maternal interactive behavior such as flexibility and toddler developmental outcomes, as indexed by play sophistication. Addressing these association differences is particularly important in children born VLBW because interventions targeting parent interaction strategies such as

  14. The Value of Multivariate Model Sophistication: An Application to pricing Dow Jones Industrial Average options

    DEFF Research Database (Denmark)

    Rombouts, Jeroen V.K.; Stentoft, Lars; Violante, Francesco

    innovation for a Laplace innovation assumption improves the pricing in a smaller way. Apart from investigating directly the value of model sophistication in terms of dollar losses, we also use the model condence set approach to statistically infer the set of models that delivers the best pricing performance.......We assess the predictive accuracy of a large number of multivariate volatility models in terms of pricing options on the Dow Jones Industrial Average. We measure the value of model sophistication in terms of dollar losses by considering a set 248 multivariate models that differer...

  15. Cognitive ability rivals the effect of political sophistication on ideological voting

    DEFF Research Database (Denmark)

    Hebbelstrup Rye Rasmussen, Stig

    2016-01-01

    This article examines the impact of cognitive ability on ideological voting. We find, using a US sample and a Danish sample, that the effect of cognitive ability rivals the effect of the traditionally strongest predicter of ideological voting political sophistication. Furthermore, the results...... are consistent with the effect of cognitive ability being partly mediated by political sophistication. Much of the effect of cognitive ability remains however and is not explained by differences in education or Openness to experience either. The implications of these results for democratic theory are discussed....

  16. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

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

  17. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Science.gov (United States)

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2017-08-08

    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  18. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plechá č, P.; Harmandaris, V.

    2016-01-01

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  19. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia

    2016-10-18

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  20. Molecular tailoring of interfaces for thin film on substrate systems

    Science.gov (United States)

    Grady, Martha Elizabeth

    Thin film on substrate systems appear most prevalently within the microelectronics industry, which demands that devices operate in smaller and smaller packages with greater reliability. The reliability of these multilayer film systems is strongly influenced by the adhesion of each of the bimaterial interfaces. During use, microelectronic components undergo thermo-mechanical cycling, which induces interfacial delaminations leading to failure of the overall device. The ability to tailor interfacial properties at the molecular level provides a mechanism to improve thin film adhesion, reliability and performance. This dissertation presents the investigation of molecular level control of interface properties in three thin film-substrate systems: photodefinable polyimide films on passivated silicon substrates, self-assembled monolayers at the interface of Au films and dielectric substrates, and mechanochemically active materials on rigid substrates. For all three materials systems, the effect of interfacial modifications on adhesion is assessed using a laser-spallation technique. Laser-induced stress waves are chosen because they dynamically load the thin film interface in a precise, noncontacting manner at high strain rates and are suitable for both weak and strong interfaces. Photodefinable polyimide films are used as dielectrics in flip chip integrated circuit packages to reduce the stress between silicon passivation layers and mold compound. The influence of processing parameters on adhesion is examined for photodefinable polyimide films on silicon (Si) substrates with three different passivation layers: silicon nitride (SiNx), silicon oxynitride (SiOxNy), and the native silicon oxide (SiO2). Interfacial strength increases when films are processed with an exposure step as well as a longer cure cycle. Additionally, the interfacial fracture energy is assessed using a dynamic delamination protocol. The high toughness of this interface (ca. 100 J/m2) makes it difficult

  1. Multi-disciplinary communication networks for skin risk assessment in nursing homes with high IT sophistication.

    Science.gov (United States)

    Alexander, Gregory L; Pasupathy, Kalyan S; Steege, Linsey M; Strecker, E Bradley; Carley, Kathleen M

    2014-08-01

    The role of nursing home (NH) information technology (IT) in quality improvement has not been clearly established, and its impacts on communication between care givers and patient outcomes in these settings deserve further attention. In this research, we describe a mixed method approach to explore communication strategies used by healthcare providers for resident skin risk in NH with high IT sophistication (ITS). Sample included NH participating in the statewide survey of ITS. We incorporated rigorous observation of 8- and 12-h shifts, and focus groups to identify how NH IT and a range of synchronous and asynchronous tools are used. Social network analysis tools and qualitative analysis were used to analyze data and identify relationships between ITS dimensions and communication interactions between care providers. Two of the nine ITS dimensions (resident care-technological and administrative activities-technological) and total ITS were significantly negatively correlated with number of unique interactions. As more processes in resident care and administrative activities are supported by technology, the lower the number of observed unique interactions. Additionally, four thematic areas emerged from staff focus groups that demonstrate how important IT is to resident care in these facilities including providing resident-centered care, teamwork and collaboration, maintaining safety and quality, and using standardized information resources. Our findings in this study confirm prior research that as technology support (resident care and administrative activities) and overall ITS increases, observed interactions between staff members decrease. Conversations during staff interviews focused on how technology facilitated resident centered care through enhanced information sharing, greater virtual collaboration between team members, and improved care delivery. These results provide evidence for improving the design and implementation of IT in long term care systems to support

  2. Molecular Physiology of Root System Architecture in Model Grasses

    Science.gov (United States)

    Hixson, K.; Ahkami, A. H.; Anderton, C.; Veličković, D.; Myers, G. L.; Chrisler, W.; Lindenmaier, R.; Fang, Y.; Yabusaki, S.; Rosnow, J. J.; Farris, Y.; Khan, N. E.; Bernstein, H. C.; Jansson, C.

    2017-12-01

    Unraveling the molecular and physiological mechanisms involved in responses of Root System Architecture (RSA) to abiotic stresses and shifts in microbiome structure is critical to understand and engineer plant-microbe-soil interactions in the rhizosphere. In this study, accessions of Brachypodium distachyon Bd21 (C3 model grass) and Setaria viridis A10.1 (C4 model grass) were grown in phytotron chambers under current and elevated CO2 levels. Detailed growth stage-based phenotypic analysis revealed different above- and below-ground morphological and physiological responses in C3 and C4 grasses to enhanced CO2 levels. Based on our preliminary results and by screening values of total biomass, water use efficiency, root to shoot ratio, RSA parameters and net assimilation rates, we postulated a three-phase physiological mechanism, i.e. RootPlus, BiomassPlus and YieldPlus phases, for grass growth under elevated CO2 conditions. Moreover, this comprehensive set of morphological and process-based observations are currently in use to develop, test, and calibrate biophysical whole-plant models and in particular to simulate leaf-level photosynthesis at various developmental stages of C3 and C4 using the model BioCro. To further link the observed phenotypic traits at the organismal level to tissue and molecular levels, and to spatially resolve the origin and fate of key metabolites involved in primary carbohydrate metabolism in different root sections, we complement root phenotypic observations with spatial metabolomics data using mass spectrometry imaging (MSI) methods. Focusing on plant-microbe interactions in the rhizosphere, six bacterial strains with plant growth promoting features are currently in use in both gel-based and soil systems to screen root growth and development in Brachypodium. Using confocal microscopy, GFP-tagged bacterial systems are utilized to study the initiation of different root types of RSA, including primary root (PR), coleoptile node axile root (CNR

  3. Assessing Epistemic Sophistication by Considering Domain-Specific Absolute and Multiplicistic Beliefs Separately

    Science.gov (United States)

    Peter, Johannes; Rosman, Tom; Mayer, Anne-Kathrin; Leichner, Nikolas; Krampen, Günter

    2016-01-01

    Background: Particularly in higher education, not only a view of science as a means of finding absolute truths (absolutism), but also a view of science as generally tentative (multiplicism) can be unsophisticated and obstructive for learning. Most quantitative epistemic belief inventories neglect this and understand epistemic sophistication as…

  4. The Relationship between Logistics Sophistication and Drivers of the Outsourcing of Logistics Activities

    Directory of Open Access Journals (Sweden)

    Peter Wanke

    2008-10-01

    Full Text Available A strong link has been established between operational excellence and the degree of sophistication of logistics organization, a function of factors such as performance monitoring, investment in Information Technology [IT] and the formalization of logistics organization, as proposed in the Bowersox, Daugherty, Dröge, Germain and Rogers (1992 Leading Edge model. At the same time, shippers have been increasingly outsourcing their logistics activities to third party providers. This paper, based on a survey with large Brazilian shippers, addresses a gap in the literature by investigating the relationship between dimensions of logistics organization sophistication and drivers of logistics outsourcing. To this end, the dimensions behind the logistics sophistication construct were first investigated. Results from factor analysis led to the identification of six dimensions of logistics sophistication. By means of multivariate logistical regression analyses it was possible to relate some of these dimensions, such as the formalization of the logistics organization, to certain drivers of the outsourcing of logistics activities of Brazilian shippers, such as cost savings. These results indicate the possibility of segmenting shippers according to characteristics of their logistics organization, which may be particularly useful to logistics service providers.

  5. Reacting to Neighborhood Cues?: Political Sophistication Moderates the Effect of Exposure to Immigrants

    DEFF Research Database (Denmark)

    Danckert, Bolette; Dinesen, Peter Thisted; Sønderskov, Kim Mannemar

    2017-01-01

    is founded on politically sophisticated individuals having a greater comprehension of news and other mass-mediated sources, which makes them less likely to rely on neighborhood cues as sources of information relevant for political attitudes. Based on a unique panel data set with fine-grained information...

  6. Sophistic Ethics in the Technical Writing Classroom: Teaching "Nomos," Deliberation, and Action.

    Science.gov (United States)

    Scott, J. Blake

    1995-01-01

    Claims that teaching ethics is particularly important to technical writing. Outlines a classical, sophistic approach to ethics based on the theories and pedagogies of Protagoras, Gorgias, and Isocrates, which emphasizes the Greek concept of "nomos," internal and external deliberation, and responsible action. Discusses problems and…

  7. Close to the Clothes : Materiality and Sophisticated Archaism in Alexander van Slobbe’s Design Practices

    NARCIS (Netherlands)

    Baronian, M.-A.

    This article looks at the work of contemporary Dutch fashion designer Alexander van Slobbe (1959) and examines how, since the 1990s, his fashion practices have consistently and consciously put forward a unique reflection on questions related to materiality, sophisticated archaism, luxury,

  8. Close to the Clothes: Materiality and Sophisticated Archaism in Alexander van Slobbe’s Design Practices

    NARCIS (Netherlands)

    Baronian, M.-A.

    This article looks at the work of contemporary Dutch fashion designer Alexander van Slobbe (1959) and examines how, since the 1990s, his fashion practices have consistently and consciously put forward a unique reflection on questions related to materiality, sophisticated archaism, luxury,

  9. Does a more sophisticated storm erosion model improve probabilistic erosion estimates?

    NARCIS (Netherlands)

    Ranasinghe, R.W.M.R.J.B.; Callaghan, D.; Roelvink, D.

    2013-01-01

    The dependency between the accuracy/uncertainty of storm erosion exceedance estimates obtained via a probabilistic model and the level of sophistication of the structural function (storm erosion model) embedded in the probabilistic model is assessed via the application of Callaghan et al.'s (2008)

  10. Spectroscopic Studies of Molecular Systems relevant in Astrobiology

    Science.gov (United States)

    Fornaro, Teresa

    2016-01-01

    In the Astrobiology context, the study of the physico-chemical interactions involving "building blocks of life" in plausible prebiotic and space-like conditions is fundamental to shed light on the processes that led to emergence of life on Earth as well as to molecular chemical evolution in space. In this PhD Thesis, such issues have been addressed both experimentally and computationally by employing vibrational spectroscopy, which has shown to be an effective tool to investigate the variety of intermolecular interactions that play a key role in self-assembling mechanisms of nucleic acid components and their binding to mineral surfaces. In particular, in order to dissect the contributions of the different interactions to the overall spectroscopic signals and shed light on the intricate experimental data, feasible computational protocols have been developed for the characterization of the spectroscopic properties of such complex systems. This study has been carried out through a multi-step strategy, starting the investigation from the spectroscopic properties of the isolated nucleobases, then studying the perturbation induced by the interaction with another molecule (molecular dimers), towards condensed phases like the molecular solid, up to the case of nucleic acid components adsorbed on minerals. A proper modeling of these weakly bound molecular systems has required, firstly, a validation of dispersion-corrected Density Functional Theory methods for simulating anharmonic vibrational properties. The isolated nucleobases and some of their dimers have been used as benchmark set for identifying a general, reliable and effective computational procedure based on fully anharmonic quantum mechanical computations of the vibrational wavenumbers and infrared intensities within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective dispersion-corrected density functional B3LYP-D3, in conjunction with basis sets of

  11. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  12. Reactive polymer coatings: A robust platform towards sophisticated surface engineering for biotechnology

    Science.gov (United States)

    Chen, Hsien-Yeh

    Functionalized poly(p-xylylenes) or so-called reactive polymers can be synthesized via chemical vapor deposition (CVD) polymerization. The resulting ultra-thin coatings are pinhole-free and can be conformally deposited to a wide range of substrates and materials. More importantly, the equipped functional groups can served as anchoring sites for tailoring the surface properties, making these reactive coatings a robust platform that can deal with sophisticated challenges faced in biointerfaces. In this work presented herein, surface coatings presenting various functional groups were prepared by CVD process. Such surfaces include aldehyde-functionalized coating to precisely immobilize saccharide molecules onto well-defined areas and alkyne-functionalized coating to click azide-modified molecules via Huisgen 1,3-dipolar cycloaddition reaction. Moreover, CVD copolymerization has been conducted to prepare multifunctional coatings and their specific functions were demonstrated by the immobilization of biotin and NHS-ester molecules. By using a photodefinable coating, polyethylene oxides were immobilized onto a wide range of substrates through photo-immobilization. Spatially controlled protein resistant properties were characterized by selective adsorption of fibrinogen and bovine serum albumin as model systems. Alternatively, surface initiator coatings were used for polymer graftings of polyethylene glycol) methyl ether methacrylate, and the resultant protein- and cell- resistant properties were characterized by adsorption of kinesin motor proteins, fibrinogen, and murine fibroblasts (NIH3T3). Accessibility of reactive coatings within confined microgeometries was systematically studied, and the preparation of homogeneous polymer thin films within the inner surface of microchannels was demonstrated. Moreover, these advanced coatings were applied to develop a dry adhesion process for microfluidic devices. This process provides (i) excellent bonding strength, (ii) extended

  13. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwagi, H [Institute for Molecular Science, Okazaki, Aichi (Japan)

    1982-06-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience.

  14. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    International Nuclear Information System (INIS)

    Kashiwagi, H.

    1982-01-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience. (orig.)

  15. The characterization of an economic and portable LED-based photoacoustic imaging system to facilitate molecular imaging

    Directory of Open Access Journals (Sweden)

    Ali Hariri

    2018-03-01

    Full Text Available Photoacoustic imaging (PAI is a non-invasive, high-resolution hybrid imaging modality that combines optical excitation and ultrasound detection. PAI can image endogenous chromophores (melanin, hemoglobin, etc. and exogenous contrast agents in different medical applications. However, most current equipment uses sophisticated and complicated OPO lasers with tuning and stability features inconsistent with broad clinical deployment. As the number of applications of PAI in medicine increases, there is an urgent need to make the imaging equipment more compact, portable, and affordable. Here, portable light emitting diode – based photoacoustic imaging (PLED-PAI was introduced and characterized in terms of system specifications, light source characterizations, photoacoustic spatial/temporal resolution, and penetration. The system uses two LED arrays attached to the sides of a conventional ultrasound transducer. The LED pulse repetition rate is tunable between 1 K Hz, 2 K Hz, 3 K Hz, and 4 K Hz. The axial resolution was 0.268 mm, and the lateral resolution was between 0.55 and 0.59 mm. The system could detect optical absorber (pencil lead at a depth of 3.2 cm and the detection limits of indocyanine green (ICG and methylene blue (MB were 9 μM and 0.78 mM. In vivo imaging of labeled human mesenchymal stem cells was achieved to confirm compatibility with small animal imaging. The characterization we report here may have value to other groups evaluating commercially available photoacoustic imaging equipment. Keywords: Portable photoacoustic imaging, LED, Optoacoustic imaging, Molecular imaging

  16. Molecular photoionization studies of nucleobases and correlated systems

    Energy Technology Data Exchange (ETDEWEB)

    Poliakoff, Erwin D. [Louisiana State Univ., Baton Rouge, LA (United States)

    2015-03-11

    We proposed molecular photoionization studies in order to probe correlated events in fundamental scattering phenomena. In particular, we suggested that joint theoretical-experimental studies would provide a window into the microscopic aspects that are of central importance in AMO and chemical physics generally, and would generate useful data for wide array of important DOE topics, such as ultrafast dynamics, high harmonic generation, and probes of nonadiabatic processes. The unifying theme is that correlations between electron scattering dynamics and molecular geometry highlight inherently molecular aspects of the photoelectron behavior.

  17. Diffracted X-ray tracking: new system for single molecular detection with X-rays

    CERN Document Server

    Sasaki, Y C; Adachi, S; Suzuki, Y; Yagi, N

    2001-01-01

    We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements.

  18. Diffracted X-ray tracking: new system for single molecular detection with X-rays

    International Nuclear Information System (INIS)

    Sasaki, Y.C.; Okumura, Y.; Adachi, S.; Suzuki, Y.; Yagi, N.

    2001-01-01

    We propose a new X-ray methodology for direct observations of the behaviors of single molecular units in real time and real space. This new system, which we call Diffracted X-ray Tracking (DXT), monitors the Brownian motions of a single molecular unit by observations of X-ray diffracted spots from a nanocrystal, tightly bound to the individual single molecular unit in bio-systems. DXT does not determine any translational movements, but only orientational movements

  19. Sophisticated Fowl: The Complex Behaviour and Cognitive Skills of Chickens and Red Junglefowl

    Directory of Open Access Journals (Sweden)

    Laura Garnham

    2018-01-01

    Full Text Available The world’s most numerous bird, the domestic chicken, and their wild ancestor, the red junglefowl, have long been used as model species for animal behaviour research. Recently, this research has advanced our understanding of the social behaviour, personality, and cognition of fowl, and demonstrated their sophisticated behaviour and cognitive skills. Here, we overview some of this research, starting with describing research investigating the well-developed senses of fowl, before presenting how socially and cognitively complex they can be. The realisation that domestic chickens, our most abundant production animal, are behaviourally and cognitively sophisticated should encourage an increase in general appraise and fascination towards them. In turn, this should inspire increased use of them as both research and hobby animals, as well as improvements in their unfortunately often poor welfare.

  20. The relation between maturity and sophistication shall be properly dealt with in nuclear power development

    International Nuclear Information System (INIS)

    Li Yongjiang

    2009-01-01

    The paper analyses the advantages and disadvantages of the second generation improved technologies and third generation technologies mainly developed in China in terms of safety and economy. The paper also discusses the maturity of the second generation improved technologies and the sophistication of the third generation technologies respectively. Meanwhile, the paper proposes that the advantage and disadvantage of second generation improved technologies and third generation technologies should be carefully taken into consideration and the relationship between the maturity and sophistication should be properly dealt with in the current stage. A two-step strategy shall be taken as a solution to solve the problem of insufficient capacity of nuclear power, trace and develop the third generation technologies, so as to ensure the sound and fast development of nuclear power. (authors)

  1. Financial Sophistication and the Distribution of the Welfare Cost of Inflation

    OpenAIRE

    Paola Boel; Gabriele Camera

    2009-01-01

    The welfare cost of anticipated inflation is quantified in a calibrated model of the U.S. economy that exhibits tractable equilibrium dispersion in wealth and earnings. Inflation does not generate large losses in societal welfare, yet its impact varies noticeably across segments of society depending also on the financial sophistication of the economy. If money is the only asset, then inflation hurts mostly the wealthier and more productive agents, while those poorer and less productive may ev...

  2. Putin’s Russia: Russian Mentality and Sophisticated Imperialism in Military Policies

    OpenAIRE

    Szénási, Lieutenant-Colonel Endre

    2016-01-01

    According to my experiences, the Western world hopelessly fails to understand Russian mentality, or misinterprets it. During my analysis of the Russian way of thinking I devoted special attention to the examination of military mentality. I have connected the issue of the Russian way of thinking to the contemporary imperial policies of Putin’s Russia.  I have also attempted to prove the level of sophistication of both. I hope that a better understanding of both the Russian mentality and imperi...

  3. Molecular Genetic and Gene Therapy Studies of the Musculoskeletal System

    National Research Council Canada - National Science Library

    Baylink, David

    2004-01-01

    The primary goal of the proposed work is to apply several state of the art molecular genetic and gene therapy technologies to address fundamental questions in bone biology with a particular emphasis on attempting: l...

  4. Ion-molecular equilibria and activity determination in the RbF-ZrF4 system

    International Nuclear Information System (INIS)

    Skokan, E.V.; Nikitin, M.I.; Sorokin, I.D.; Korenev, Yu.M.; Sidorov, L.N.

    1983-01-01

    Activity of zirconium tetrofluoride in 100-33.3 mol % ZrF 4 concentration range was determined during isothermal evaporation of samples of different initial composition of RbF-ZrF 4 system, using ion-molecular equilibrium method. It became possible, using the exchange ion-molecular reactions to determine ZrF 4 activity approximately 10 -10 in the region of state diagram of RbF-ZrF 4 system, adjoining to rubidium fluoride. The comparative analysis of results, obtained by the methods of isothermal evaporation, ion-molecular equilibria is given; the advantages and restrictions of ion-molecular equilibrium method are presented

  5. Optimization of fuel ethanol recovery systems using molecular sieves

    International Nuclear Information System (INIS)

    Scheller, W.A.

    1989-01-01

    The use of molecular sieves for the dehydration of rectified fuel ethanol requires only about 58% of the energy required by azeotropic distillation, the usual commercial process. Recently molecular sieve prices have become low enough that their use can be economically competitive with azeotropic distillation. This paper contains results of mass and energy balances to determine the water content of the rectified ethanol (6.15 weight percent) that will result in the minimum energy requirement for producing anhydrous ethanol with the molecular sieve process and byproduct distillers soluble syrup from fermented corn mash containing 7.23 weight percent ethanol. In this paper results of economic evaluations to determine the water content of the rectified ethanol (7.58 weight percent) which results in a minimum investment and operating cost are presented

  6. Subtle Monte Carlo Updates in Dense Molecular Systems

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Boomsma, Wouter; Johansson, Kristoffer E.

    2012-01-01

    Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce...... as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results...... suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions....

  7. Kinetic theory of beam-induced plasmas generalised to sophisticated atomic structures

    International Nuclear Information System (INIS)

    Peyraud-Cuenca, Nelly

    1987-01-01

    We present an analytic kinetic model available for all particle-beam-induced atomic plasmas, without any restriction on the distribution of electronic levels. The method is an iteration of the already known solution available only for the distribution of atomic levels as in the rare gases. We recall a universal atomic kinetic model which, independently of its applications to the study of efficient laser systems, might be a first step in the analytic investigation of molecular problems. Then, the iteration is systematically applied to all possible atomic structures whose number is increased by the non-local character of inelastic processes. We deduce a general analytic representation of the 'tail' of the electron distribution function as a ratio between non-local source terms and a combination of inelastic cross sections, from which we exhibit a physical interpretation and essential scaling laws. The theory is applied to sodium which is an important element in the research of efficient laser systems. (author)

  8. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  9. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  10. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis

    2017-10-03

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

  11. Environmental Molecular Sciences Laboratory Operations System: Version 4.0 - system requirements specification

    Energy Technology Data Exchange (ETDEWEB)

    Kashporenko, D.

    1996-07-01

    This document is intended to provide an operations standard for the Environmental Molecular Sciences Laboratory OPerations System (EMSL OPS). It is directed toward three primary audiences: (1) Environmental Molecular Sciences Laboratory (EMSL) facility and operations personnel; (2) laboratory line managers and staff; and (3) researchers, equipment operators, and laboratory users. It is also a statement of system requirements for software developers of EMSL OPS. The need for a finely tuned, superior research environment as provided by the US Department of Energy`s (DOE) Environmental Molecular Sciences Laboratory has never been greater. The abrupt end of the Cold War and the realignment of national priorities caused major US and competing overseas laboratories to reposition themselves in a highly competitive research marketplace. For a new laboratory such as the EMSL, this means coming into existence in a rapidly changing external environment. For any major laboratory, these changes create funding uncertainties and increasing global competition along with concomitant demands for higher standards of research product quality and innovation. While more laboratories are chasing fewer funding dollars, research ideas and proposals, especially for molecular-level research in the materials and biological sciences, are burgeoning. In such an economically constrained atmosphere, reduced costs, improved productivity, and strategic research project portfolio building become essential to establish and maintain any distinct competitive advantage. For EMSL, this environment and these demands require clear operational objectives, specific goals, and a well-crafted strategy. Specific goals will evolve and change with the evolution of the nature and definition of DOE`s environmental research needs. Hence, EMSL OPS is designed to facilitate migration of these changes with ease into every pertinent job function, creating a facile {open_quotes}learning organization.{close_quotes}

  12. Molecular materials and devices: developing new functional systems based on the coordination chemistry approach

    Directory of Open Access Journals (Sweden)

    Toma Henrique E.

    2003-01-01

    Full Text Available At the onset of the nanotechnology age, molecular designing of materials and single molecule studies are opening wide possibilities of using molecular systems in electronic and photonic devices, as well as in technological applications based on molecular switching or molecular recognition. In this sense, inorganic chemists are privileged by the possibility of using the basic strategies of coordination chemistry to build up functional supramolecular materials, conveying the remarkable chemical properties of the metal centers and the characteristics of the ancillary ligands. Coordination chemistry also provides effective self-assembly strategies based on specific metal-ligand affinity and stereochemistry. Several molecular based materials, derived from inorganic and metal-organic compounds are focused on this article, with emphasis on new supramolecular porphyrins and porphyrazines, metal-clusters and metal-polyimine complexes. Such systems are also discussed in terms of their applications in catalysis, sensors and molecular devices.

  13. The Physics of Coupled Atomic-Molecular Condensate System

    Science.gov (United States)

    2010-10-09

    electric dipoles represents a novel state of matter with long-range and anisotropic dipole-dipole interactions, that are highly amenable to the...free-bound FC factor. Simultaneously, a series of laser �elds of (molecular) Rabi frequency i (i 2) are applied to move the molecules from the

  14. Do organizations adopt sophisticated capital budgeting practices to deal with uncertainty in the investment decision? : A research note

    NARCIS (Netherlands)

    Verbeeten, Frank H M

    This study examines the impact of uncertainty on the sophistication of capital budgeting practices. While the theoretical applications of sophisticated capital budgeting practices (defined as the use of real option reasoning and/or game theory decision rules) have been well documented, empirical

  15. "SOCRATICS" AS ADDRESSES OF ISOCRATES’ EPIDEICTIC SPEECHES (Against the Sophists, Encomium of Helen, Busiris

    Directory of Open Access Journals (Sweden)

    Anna Usacheva

    2012-06-01

    Full Text Available This article analyses the three epideictic orations of Isocrates which are in themselves a precious testimony of the quality of intellectual life at the close of the fourth century before Christ. To this period belong also the Socratics who are generally seen as an important link between Socrates and Plato. The author of this article proposes a more productive approach to the study of Antisthenes, Euclid of Megara and other so-called Socratics, revealing them not as independent thinkers but rather as adherents of the sophistic school and also as teachers, thereby, including them among those who took part in the educative activity of their time

  16. Integrative pathway knowledge bases as a tool for systems molecular medicine.

    Science.gov (United States)

    Liang, Mingyu

    2007-08-20

    There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

  17. A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

    Science.gov (United States)

    Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

    2011-01-01

    Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

  18. Exploring coherent transport through π-stacked systems for molecular electronic devices

    DEFF Research Database (Denmark)

    Li, Qian; Solomon, Gemma

    2014-01-01

    Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron trans...

  19. The 'deep' independent system operator. A new sophisticated institutional design for system operators in the 3rd energy package of September 2007 in comparison to the Proposal of the 8 EC-Member States for a Directive of the EP and the Council amending Directive 2003/54/EC concerning common rules for the internal market in electricity and repealing Directive 96/92/EC. A German perspective on implementing an effective and efficient unbundling of Transmission System Operator

    International Nuclear Information System (INIS)

    Saecker, F.J.

    2008-01-01

    The ownership unbundling-model and the 'deep' ISO-model (ISO stands for Independent System Operator) are not compatible with the EC-Treaty, if they were realized against the interest of the shareholder's assembly. The proposal of the eight EC member states for an effective and efficient unbundling avoids the constitutional problems and strengthens the independence of transmission system operators

  20. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  1. Molecular and supramolecular speciation of monoamide extractant systems

    International Nuclear Information System (INIS)

    Ferru, G.

    2012-01-01

    DEHiBA (N,N-di-(ethyl-2-hexyl)isobutyramide, a monoamide, was chosen as selective extractant for the recovery of uranium in the first cycle of the GANEX process, which aims to realize the grouped extraction of actinides in the second step of the process. The aim of this work is an improved description of monoamide organic solutions in alkane diluent after solutes extraction: water, nitric acid and uranyl nitrate. A parametric study was undertaken to characterize species at molecular scale (by IR spectroscopy, UV-visible spectroscopy, time-resolved laser-induced fluorescence spectroscopy, and electro-spray ionisation mass spectrometry) and at supramolecular scale (by vapor pressure osmometry and small angle X-ray scattering coupled to molecular dynamic simulations). Extraction isotherms were modelled taking into account the molecular and supramolecular speciation. These works showed that the organization of the organic solution depends on the amide concentration, the nature and the concentration of the extracted solute. Three regimes can be distinguished. 1/For extractant concentration less than 0.5 mol/L, monomers are predominate species. 2/ For extractant concentrations between 0.5 and 1 mol/L, small aggregates are formed containing 2 to 4 molecules of monoamide. 3/ For more concentrated solutions (greater than 1 mol/L), slightly larger species can be formed after water or nitric acid extraction. Concerning uranyl nitrate extraction, an important and strong organization of the organic phase is observed, which no longer allows the formation of well spherical defined aggregates. At molecular scale, complexes are not sensitive to the organization of the solution: the same species are observed, regardless of the solute and extractant concentrations in organic phase. (author) [fr

  2. Systematization and sophistication of a comprehensive sensitivity analysis program. Phase 2

    International Nuclear Information System (INIS)

    Oyamada, Kiyoshi; Ikeda, Takao

    2004-02-01

    This study developed minute estimation by adopting comprehensive sensitivity analytical program for reliability of TRU waste repository concepts in a crystalline rock condition. We examined each components and groundwater scenario of geological repository and prepared systematic bases to examine the reliability from the point of comprehensiveness. Models and data are sophisticated to examine the reliability. Based on an existing TRU waste repository concepts, effects of parameters to nuclide migration were quantitatively classified. Those parameters, that will be decided quantitatively, are such as site character of natural barrier and design specification of engineered barriers. Considering the feasibility of those figures of specifications, reliability is re-examined on combinations of those parameters within a practical range. Future issues are; Comprehensive representation of hybrid geosphere model including the fractured medium and permeable matrix medium. Sophistication of tools to develop the reliable combinations of parameters. It is significant to continue this study because the disposal concepts and specification of TRU nuclides containing waste on various sites shall be determined rationally and safely through these studies. (author)

  3. Electronic effects and fundamental physics studied in molecular interfaces.

    Science.gov (United States)

    Pope, Thomas; Du, Shixuan; Gao, Hong-Jun; Hofer, Werner A

    2018-05-29

    Scanning probe instruments in conjunction with a very low temperature environment have revolutionized the ability of building, functionalizing, and analysing two dimensional interfaces in the last twenty years. In addition, the availability of fast, reliable, and increasingly sophisticated methods to simulate the structure and dynamics of these interfaces allow us to capture even very small effects at the atomic and molecular level. In this review we shall focus largely on metal surfaces and organic molecular compounds and show that building systems from the bottom up and controlling the physical properties of such systems is no longer within the realm of the desirable, but has become day to day reality in our best laboratories.

  4. Molecular-beam epitaxial growth and ion-beam analysis systems for functional materials research

    International Nuclear Information System (INIS)

    Takeshita, H.; Aoki, Y.; Yamamoto, S.; Naramoto, H.

    1992-01-01

    Experimental systems for molecular beam epitaxial growth and ion beam analysis have been designed and constructed for the research of inorganic functional materials such as thin films and superlattices. (author)

  5. Materials learning from life: concepts for active, adaptive and autonomous molecular systems.

    Science.gov (United States)

    Merindol, Rémi; Walther, Andreas

    2017-09-18

    Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed life provides the best demonstrations of complex and functional out-of-equilibrium systems: cells keep track of time, communicate, move, adapt, evolve and replicate continuously. Stirred by the understanding of biological principles, artificial out-of-equilibrium systems are emerging in many fields of soft matter science. Here we put in perspective the molecular mechanisms driving biological functions with the ones driving synthetic molecular systems. Focusing on principles that enable new levels of functionalities (temporal control, autonomous structures, motion and work generation, information processing) rather than on specific material classes, we outline key cross-disciplinary concepts that emerge in this challenging field. Ultimately, the goal is to inspire and support new generations of autonomous and adaptive molecular devices fueled by self-regulating chemistry.

  6. Pulse radiolysis studies of fast reactions in molecular systems. Progress report, November 1976--October 1977

    International Nuclear Information System (INIS)

    Dorfman, L.M.

    1977-01-01

    Results from research in the following two areas are given: formation, properties, and reactivity of molecular ionic species in irradiated liquid systems; and pulse radiolysis of elementary reactions in protein function

  7. Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

    Science.gov (United States)

    EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

  8. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plechac, Petr

    2017-01-01

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from

  9. Molecular quenching and relaxation in a plasmonic tunable system

    Science.gov (United States)

    Baffou, Guillaume; Girard, Christian; Dujardin, Erik; Colas Des Francs, Gérard; Martin, Olivier J. F.

    2008-03-01

    Molecular fluorescence decay is significantly modified when the emitting molecule is located near a plasmonic structure. When the lateral sizes of such structures are reduced to nanometer-scale cross sections, they can be used to accurately control and amplify the emission rate. In this Rapid Communication, we extend Green’s dyadic method to quantitatively investigate both radiative and nonradiative decay channels experienced by a single fluorescent molecule confined in an adjustable dielectric-metal nanogap. The technique produces data in excellent agreement with current experimental work.

  10. Mixed 2D molecular systems: Mechanic, thermodynamic and dielectric properties

    Energy Technology Data Exchange (ETDEWEB)

    Beno, Juraj [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Weis, Martin [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)], E-mail: Martin.Weis@stuba.sk; Dobrocka, Edmund [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Institute of Electrical Engineering, Slovak Academy of Sciences, Dubravska cesta 9, 841 04-SK Bratislava (Slovakia); Hasko, Daniel [International Laser Centre, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)

    2008-08-15

    Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms ({pi}-A), the Maxwell displacement current (MDC) measurement, X-ray reflectivity (XRR) and atomic force microscopy (AFM) to investigate the selected mechanic, thermodynamic and dielectric properties based on orientational structure of monolayers. On the base of {pi}-A isotherms analysis we explain the creation of stable structures and found optimal monolayer composition. The dielectric properties represented by MDC generated monolayers were analyzed in terms of excess dipole moment, proposing the effect of dipole-dipole interaction. XRR and AFM results illustrate deposited film structure and molecular ordering.

  11. Raman spectroscopy on simple molecular systems at very high density

    International Nuclear Information System (INIS)

    Schiferl, D.; LeSar, R.S.; Moore, D.S.

    1988-01-01

    We present an overview of how Raman spectroscopy is done on simple molecular substances at high pressures. Raman spectroscopy is one of the most powerful tools for studying these substances. It is often the quickest means to explore changes in crystal and molecular structures, changes in bond strength, and the formation of new chemical species. Raman measurements have been made at pressures up to 200 GPa (2 Mbar). Even more astonishing is the range of temperatures (4-5200/degree/K) achieved in various static and dynamic (shock-wave) pressure experiments. One point we particularly wish to emphasize is the need for a good theoretical understanding to properly interpret and use experimental results. This is particularly true at ultra-high pressures, where strong crystal field effects can be misinterpreted as incipient insulator-metal transitions. We have tried to point out apparatus, techniques, and results that we feel are particularly noteworthy. We have also included some of the /open quotes/oral tradition/close quotes/ of high pressure Raman spectroscopy -- useful little things that rarely or never appear in print. Because this field is rapidly expanding, we discuss a number of exciting new techniques that have been informally communicated to us, especially those that seem to open new possibilities. 58 refs., 18 figs

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-21

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

  13. Controlling Motion at the Nanoscale: Rise of the Molecular Machines.

    Science.gov (United States)

    Abendroth, John M; Bushuyev, Oleksandr S; Weiss, Paul S; Barrett, Christopher J

    2015-08-25

    As our understanding and control of intra- and intermolecular interactions evolve, ever more complex molecular systems are synthesized and assembled that are capable of performing work or completing sophisticated tasks at the molecular scale. Commonly referred to as molecular machines, these dynamic systems comprise an astonishingly diverse class of motifs and are designed to respond to a plethora of actuation stimuli. In this Review, we outline the conditions that distinguish simple switches and rotors from machines and draw from a variety of fields to highlight some of the most exciting recent examples of opportunities for driven molecular mechanics. Emphasis is placed on the need for controllable and hierarchical assembly of these molecular components to display measurable effects at the micro-, meso-, and macroscales. As in Nature, this strategy will lead to dramatic amplification of the work performed via the collective action of many machines organized in linear chains, on functionalized surfaces, or in three-dimensional assemblies.

  14. xSyn: A Software Tool for Identifying Sophisticated 3-Way Interactions From Cancer Expression Data

    Directory of Open Access Journals (Sweden)

    Baishali Bandyopadhyay

    2017-08-01

    Full Text Available Background: Constructing gene co-expression networks from cancer expression data is important for investigating the genetic mechanisms underlying cancer. However, correlation coefficients or linear regression models are not able to model sophisticated relationships among gene expression profiles. Here, we address the 3-way interaction that 2 genes’ expression levels are clustered in different space locations under the control of a third gene’s expression levels. Results: We present xSyn, a software tool for identifying such 3-way interactions from cancer gene expression data based on an optimization procedure involving the usage of UPGMA (Unweighted Pair Group Method with Arithmetic Mean and synergy. The effectiveness is demonstrated by application to 2 real gene expression data sets. Conclusions: xSyn is a useful tool for decoding the complex relationships among gene expression profiles. xSyn is available at http://www.bdxconsult.com/xSyn.html .

  15. When not to copy: female fruit flies use sophisticated public information to avoid mated males

    Science.gov (United States)

    Loyau, Adeline; Blanchet, Simon; van Laere, Pauline; Clobert, Jean; Danchin, Etienne

    2012-10-01

    Semen limitation (lack of semen to fertilize all of a female's eggs) imposes high fitness costs to female partners. Females should therefore avoid mating with semen-limited males. This can be achieved by using public information extracted from watching individual males' previous copulating activities. This adaptive preference should be flexible given that semen limitation is temporary. We first demonstrate that the number of offspring produced by males Drosophila melanogaster gradually decreases over successive copulations. We then show that females avoid mating with males they just watched copulating and that visual public cues are sufficient to elicit this response. Finally, after males were given the time to replenish their sperm reserves, females did not avoid the males they previously saw copulating anymore. These results suggest that female fruit flies may have evolved sophisticated behavioural processes of resistance to semen-limited males, and demonstrate unsuspected adaptive context-dependent mate choice in an invertebrate.

  16. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  17. Water activity in liquid food systems: A molecular scale interpretation.

    Science.gov (United States)

    Maneffa, Andrew J; Stenner, Richard; Matharu, Avtar S; Clark, James H; Matubayasi, Nobuyuki; Shimizu, Seishi

    2017-12-15

    Water activity has historically been and continues to be recognised as a key concept in the area of food science. Despite its ubiquitous utilisation, it still appears as though there is confusion concerning its molecular basis, even within simple, single component solutions. Here, by close examination of the well-known Norrish equation and subsequent application of a rigorous statistical theory, we are able to shed light on such an origin. Our findings highlight the importance of solute-solute interactions thus questioning traditional, empirically based "free water" and "water structure" hypotheses. Conversely, they support the theory of "solute hydration and clustering" which advocates the interplay of solute-solute and solute-water interactions but crucially, they do so in a manner which is free of any estimations and approximations. Copyright © 2017. Published by Elsevier Ltd.

  18. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  19. A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations.

    Science.gov (United States)

    Ward, Jodie; Gilmore, Simon R; Robertson, James; Peakall, Rod

    2009-11-01

    Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA-based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single-nucleotide polymorphisms were utilized as molecular markers for subfamily to species-level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated "proof of concept" of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.

  20. The rise of a novel classification system for endometrial carcinoma; integration of molecular subclasses.

    Science.gov (United States)

    McAlpine, Jessica; Leon-Castillo, Alicia; Bosse, Tjalling

    2018-04-01

    Endometrial cancer is a clinically heterogeneous disease and it is becoming increasingly clear that this heterogeneity may be a function of the diversity of the underlying molecular alterations. Recent large-scale genomic studies have revealed that endometrial cancer can be divided into at least four distinct molecular subtypes, with well-described underlying genomic aberrations. These subtypes can be reliably delineated and carry significant prognostic as well as predictive information; embracing and incorporating them into clinical practice is thus attractive. The road towards the integration of molecular features into current classification systems is not without obstacles. Collaborative studies engaging research teams from across the world are working to define pragmatic assays, improve risk stratification systems by combining molecular features and traditional clinicopathological parameters, and determine how molecular classification can be optimally utilized to direct patient care. Pathologists and clinicians caring for women with endometrial cancer need to engage with and understand the possibilities and limitations of this new approach, because integration of molecular classification of endometrial cancers is anticipated to become an essential part of gynaecological pathology practice. This review will describe the challenges in current systems of endometrial carcinoma classification, the evolution of new molecular technologies that define prognostically distinct molecular subtypes, and potential applications of molecular classification as a step towards precision medicine and refining care for individuals with the most common gynaecological cancer in the developed world. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  1. Marine molecular biology: An emerging field of biological sciences

    Digital Repository Service at National Institute of Oceanography (India)

    Thakur, N.L.; Jain, R.; Natalio, F.; Hamer, B.; Thakur, A.N.; Muller, W.E.G.

    An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies...

  2. Calculation on uranium carbon oxygen system molecular structure by DFT

    International Nuclear Information System (INIS)

    Zhang Guangfeng; Wang Xiaolin; Zou Lexi; Sun Ying; Xue Weidong; Zhu Zhenghe; Wang Hongyan

    2001-01-01

    The authors study on the possible molecular structures U-C-O, U-O-C, C-U-O (angular structure C a nd linear structure C ∞υ ) of carbon monoxide interacting on uranium metal surface by Density functional theory (DFT). The uranium atom is used RECP (Relativistic Effective Core Potential) and contracted valence basis sets (6s5p2d4f)/[3s3p2d2f], and for carbon and oxygen atoms all are 6-311G basis sets. The author presents the results of energy optimum which shows that triple and quintuple state are more stable. The authors get the electronic state, geometry structure, energy, harmonic frequency, mechanical property, etc. of these twelve triple and quintuple state relative stable structures. The normal vibrational analytical figure of angular structure (C s ) and linear structure (C ∞υ ) is given at the same time. It is indicated that angular structure has lower energy than linear structure, moreover the angular structure of U-C-O( 3 A ) has the lowest energy. The bond strength between uranium atom and carbon monoxide is weak and between uranium atom and oxygen atom is slightly stronger than between uranium atom and carbon atom which the authors can know by superposition population and bond energy analysis among atoms

  3. Molecular characterization of the thioredoxin system from Methanosarcina acetivorans

    OpenAIRE

    McCarver, Addison C.; Lessner, Daniel J.

    2014-01-01

    The thioredoxin system, composed of thioredoxin reductase (TrxR) and thioredoxin (Trx), is widely distributed in nature, where it serves key roles in electron transfer and in defense against oxidative stress. Although recent evidence reveals Trx homologues are almost universally present among the methane-producing archaea (methanogens), a complete thioredoxin system has not been characterized from any methanogen. We examined the phylogeny of Trx homologues among methanogens and characterized ...

  4. Molecular spectral imaging system for quantitative immunohistochemical analysis of early diabetic retinopathy.

    Science.gov (United States)

    Li, Qingli; Zhang, Jingfa; Wang, Yiting; Xu, Guoteng

    2009-12-01

    A molecular spectral imaging system has been developed based on microscopy and spectral imaging technology. The system is capable of acquiring molecular spectral images from 400 nm to 800 nm with 2 nm wavelength increments. The basic principles, instrumental systems, and system calibration method as well as its applications for the calculation of the stain-uptake by tissues are introduced. As a case study, the system is used for determining the pathogenesis of diabetic retinopathy and evaluating the therapeutic effects of erythropoietin. Some molecular spectral images of retinal sections of normal, diabetic, and treated rats were collected and analyzed. The typical transmittance curves of positive spots stained for albumin and advanced glycation end products are retrieved from molecular spectral data with the spectral response calibration algorithm. To explore and evaluate the protective effect of erythropoietin (EPO) on retinal albumin leakage of streptozotocin-induced diabetic rats, an algorithm based on Beer-Lambert's law is presented. The algorithm can assess the uptake by histologic retinal sections of stains used in quantitative pathology to label albumin leakage and advanced glycation end products formation. Experimental results show that the system is helpful for the ophthalmologist to reveal the pathogenesis of diabetic retinopathy and explore the protective effect of erythropoietin on retinal cells of diabetic rats. It also highlights the potential of molecular spectral imaging technology to provide more effective and reliable diagnostic criteria in pathology.

  5. Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine.

    Science.gov (United States)

    Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

    2014-10-20

    The N≡N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    International Nuclear Information System (INIS)

    Li, King C.P.

    2009-01-01

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  7. All-organic microelectromechanical systems integrating specific molecular recognition--a new generation of chemical sensors.

    Science.gov (United States)

    Ayela, Cédric; Dubourg, Georges; Pellet, Claude; Haupt, Karsten

    2014-09-03

    Cantilever-type all-organic microelectromechanical systems based on molecularly imprinted polymers for specific analyte recognition are used as chemical sensors. They are produced by a simple spray-coating-shadow-masking process. Analyte binding to the cantilever generates a measurable change in its resonance frequency. This allows label-free detection by direct mass sensing of low-molecular-weight analytes at nanomolar concentrations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Simulation of Molecular Transport in Systems Containing Mobile Obstacles.

    Science.gov (United States)

    Polanowski, Piotr; Sikorski, Andrzej

    2016-08-04

    In this paper, we investigate the movement of molecules in crowded environments with obstacles undergoing Brownian motion by means of extensive Monte Carlo simulations. Our investigations were performed using the dynamic lattice liquid model, which was based on the cooperative movement concept and allowed to mimic systems at high densities where the motion of all elements (obstacles as well as moving particles) were highly correlated. The crowded environments are modeled on a two-dimensional triangular lattice containing obstacles (particles whose mobility was significantly reduced) moving by a Brownian motion. The subdiffusive motion of both elements in the system was analyzed. It was shown that the percolation transition does not exist in such systems in spite of the cooperative character of the particles' motion. The reduction of the obstacle mobility leads to the longer caging of liquid particles by mobile obstacles.

  9. A Strategy to Suppress Phonon Transport in Molecular Junctions Using pi-Stacked Systems

    DEFF Research Database (Denmark)

    Li, Qian; Strange, Mikkel; Duchemin, Ivan

    2017-01-01

    to suppress phonon transport in graphene-based molecular junctions preserving high electronic power factor, using nonbonded pi-stackal systems. Using first-principles calculations, we find that the thermal conductance of pi-stacked systems can be reduced by about 95%, compared with that of a covalently bonded...

  10. Fulminant hepatic failure following marijuana drug abuse: Molecular adsorbent recirculation system therapy

    Directory of Open Access Journals (Sweden)

    G Swarnalatha

    2013-01-01

    Full Text Available Marijuana is used for psychoactive and recreational purpose. We report a case of fulminant hepatic failure following marijuana drug abuse who recovered following artificial support systems for acute liver failure. There is no published literature of management of marijuana intoxication with molecular adsorbent recirculation system (MARS. MARS is effective and safe in patients with fulminant hepatic failure following marijuana intoxication.

  11. Relativistic Green function for atomic and molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Gruzdev, P.F.; Sherstyuk, A.I.

    1981-12-01

    The problem on Green function construction of Dirac equation is solved for a wide class of single electron potentials in the atom and molecule theory. The solution is obtained in the form of a spectrum analysis according to the total system of eigenfuctions of the generalized Dirac problem for eigenvalues. The problem possesses a purely discrete spectrum.

  12. Yersinia virulence factors - a sophisticated arsenal for combating host defences [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Steve Atkinson

    2016-06-01

    Full Text Available The human pathogens Yersinia pseudotuberculosis and Yersinia enterocolitica cause enterocolitis, while Yersinia pestis is responsible for pneumonic, bubonic, and septicaemic plague. All three share an infection strategy that relies on a virulence factor arsenal to enable them to enter, adhere to, and colonise the host while evading host defences to avoid untimely clearance. Their arsenal includes a number of adhesins that allow the invading pathogens to establish a foothold in the host and to adhere to specific tissues later during infection. When the host innate immune system has been activated, all three pathogens produce a structure analogous to a hypodermic needle. In conjunction with the translocon, which forms a pore in the host membrane, the channel that is formed enables the transfer of six ‘effector’ proteins into the host cell cytoplasm. These proteins mimic host cell proteins but are more efficient than their native counterparts at modifying the host cell cytoskeleton, triggering the host cell suicide response. Such a sophisticated arsenal ensures that yersiniae maintain the upper hand despite the best efforts of the host to counteract the infecting pathogen.

  13. The Impact of Services on Economic Complexity: Service Sophistication as Route for Economic Growth.

    Science.gov (United States)

    Stojkoski, Viktor; Utkovski, Zoran; Kocarev, Ljupco

    2016-01-01

    Economic complexity reflects the amount of knowledge that is embedded in the productive structure of an economy. By combining tools from network science and econometrics, a robust and stable relationship between a country's productive structure and its economic growth has been established. Here we report that not only goods but also services are important for predicting the rate at which countries will grow. By adopting a terminology which classifies manufactured goods and delivered services as products, we investigate the influence of services on the country's productive structure. In particular, we provide evidence that complexity indices for services are in general higher than those for goods, which is reflected in a general tendency to rank countries with developed service sector higher than countries with economy centred on manufacturing of goods. By focusing on country dynamics based on experimental data, we investigate the impact of services on the economic complexity of countries measured in the product space (consisting of both goods and services). Importantly, we show that diversification of service exports and its sophistication can provide an additional route for economic growth in both developing and developed countries.

  14. Exploring the predictive power of interaction terms in a sophisticated risk equalization model using regression trees.

    Science.gov (United States)

    van Veen, S H C M; van Kleef, R C; van de Ven, W P M M; van Vliet, R C J A

    2018-02-01

    This study explores the predictive power of interaction terms between the risk adjusters in the Dutch risk equalization (RE) model of 2014. Due to the sophistication of this RE-model and the complexity of the associations in the dataset (N = ~16.7 million), there are theoretically more than a million interaction terms. We used regression tree modelling, which has been applied rarely within the field of RE, to identify interaction terms that statistically significantly explain variation in observed expenses that is not already explained by the risk adjusters in this RE-model. The interaction terms identified were used as additional risk adjusters in the RE-model. We found evidence that interaction terms can improve the prediction of expenses overall and for specific groups in the population. However, the prediction of expenses for some other selective groups may deteriorate. Thus, interactions can reduce financial incentives for risk selection for some groups but may increase them for others. Furthermore, because regression trees are not robust, additional criteria are needed to decide which interaction terms should be used in practice. These criteria could be the right incentive structure for risk selection and efficiency or the opinion of medical experts. Copyright © 2017 John Wiley & Sons, Ltd.

  15. The State of Nursing Home Information Technology Sophistication in Rural and Nonrural US Markets.

    Science.gov (United States)

    Alexander, Gregory L; Madsen, Richard W; Miller, Erin L; Wakefield, Douglas S; Wise, Keely K; Alexander, Rachel L

    2017-06-01

    To test for significant differences in information technology sophistication (ITS) in US nursing homes (NH) based on location. We administered a primary survey January 2014 to July 2015 to NH in each US state. The survey was cross-sectional and examined 3 dimensions (IT capabilities, extent of IT use, degree of IT integration) among 3 domains (resident care, clinical support, administrative activities) of ITS. ITS was broken down by NH location. Mean responses were compared across 4 NH categories (Metropolitan, Micropolitan, Small Town, and Rural) for all 9 ITS dimensions and domains. Least square means and Tukey's method were used for multiple comparisons. Methods yielded 815/1,799 surveys (45% response rate). In every health care domain (resident care, clinical support, and administrative activities) statistical differences in facility ITS occurred in larger (metropolitan or micropolitan) and smaller (small town or rural) populated areas. This study represents the most current national assessment of NH IT since 2004. Historically, NH IT has been used solely for administrative activities and much less for resident care and clinical support. However, results are encouraging as ITS in other domains appears to be greater than previously imagined. © 2016 National Rural Health Association.

  16. Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task.

    Science.gov (United States)

    Akam, Thomas; Costa, Rui; Dayan, Peter

    2015-12-01

    The recently developed 'two-step' behavioural task promises to differentiate model-based from model-free reinforcement learning, while generating neurophysiologically-friendly decision datasets with parametric variation of decision variables. These desirable features have prompted its widespread adoption. Here, we analyse the interactions between a range of different strategies and the structure of transitions and outcomes in order to examine constraints on what can be learned from behavioural performance. The task involves a trade-off between the need for stochasticity, to allow strategies to be discriminated, and a need for determinism, so that it is worth subjects' investment of effort to exploit the contingencies optimally. We show through simulation that under certain conditions model-free strategies can masquerade as being model-based. We first show that seemingly innocuous modifications to the task structure can induce correlations between action values at the start of the trial and the subsequent trial events in such a way that analysis based on comparing successive trials can lead to erroneous conclusions. We confirm the power of a suggested correction to the analysis that can alleviate this problem. We then consider model-free reinforcement learning strategies that exploit correlations between where rewards are obtained and which actions have high expected value. These generate behaviour that appears model-based under these, and also more sophisticated, analyses. Exploiting the full potential of the two-step task as a tool for behavioural neuroscience requires an understanding of these issues.

  17. Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task

    Science.gov (United States)

    Akam, Thomas; Costa, Rui; Dayan, Peter

    2015-01-01

    The recently developed ‘two-step’ behavioural task promises to differentiate model-based from model-free reinforcement learning, while generating neurophysiologically-friendly decision datasets with parametric variation of decision variables. These desirable features have prompted its widespread adoption. Here, we analyse the interactions between a range of different strategies and the structure of transitions and outcomes in order to examine constraints on what can be learned from behavioural performance. The task involves a trade-off between the need for stochasticity, to allow strategies to be discriminated, and a need for determinism, so that it is worth subjects’ investment of effort to exploit the contingencies optimally. We show through simulation that under certain conditions model-free strategies can masquerade as being model-based. We first show that seemingly innocuous modifications to the task structure can induce correlations between action values at the start of the trial and the subsequent trial events in such a way that analysis based on comparing successive trials can lead to erroneous conclusions. We confirm the power of a suggested correction to the analysis that can alleviate this problem. We then consider model-free reinforcement learning strategies that exploit correlations between where rewards are obtained and which actions have high expected value. These generate behaviour that appears model-based under these, and also more sophisticated, analyses. Exploiting the full potential of the two-step task as a tool for behavioural neuroscience requires an understanding of these issues. PMID:26657806

  18. Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task.

    Directory of Open Access Journals (Sweden)

    Thomas Akam

    2015-12-01

    Full Text Available The recently developed 'two-step' behavioural task promises to differentiate model-based from model-free reinforcement learning, while generating neurophysiologically-friendly decision datasets with parametric variation of decision variables. These desirable features have prompted its widespread adoption. Here, we analyse the interactions between a range of different strategies and the structure of transitions and outcomes in order to examine constraints on what can be learned from behavioural performance. The task involves a trade-off between the need for stochasticity, to allow strategies to be discriminated, and a need for determinism, so that it is worth subjects' investment of effort to exploit the contingencies optimally. We show through simulation that under certain conditions model-free strategies can masquerade as being model-based. We first show that seemingly innocuous modifications to the task structure can induce correlations between action values at the start of the trial and the subsequent trial events in such a way that analysis based on comparing successive trials can lead to erroneous conclusions. We confirm the power of a suggested correction to the analysis that can alleviate this problem. We then consider model-free reinforcement learning strategies that exploit correlations between where rewards are obtained and which actions have high expected value. These generate behaviour that appears model-based under these, and also more sophisticated, analyses. Exploiting the full potential of the two-step task as a tool for behavioural neuroscience requires an understanding of these issues.

  19. A sophisticated simulation for the fracture behavior of concrete material using XFEM

    Science.gov (United States)

    Zhai, Changhai; Wang, Xiaomin; Kong, Jingchang; Li, Shuang; Xie, Lili

    2017-10-01

    The development of a powerful numerical model to simulate the fracture behavior of concrete material has long been one of the dominant research areas in earthquake engineering. A reliable model should be able to adequately represent the discontinuous characteristics of cracks and simulate various failure behaviors under complicated loading conditions. In this paper, a numerical formulation, which incorporates a sophisticated rigid-plastic interface constitutive model coupling cohesion softening, contact, friction and shear dilatation into the XFEM, is proposed to describe various crack behaviors of concrete material. An effective numerical integration scheme for accurately assembling the contribution to the weak form on both sides of the discontinuity is introduced. The effectiveness of the proposed method has been assessed by simulating several well-known experimental tests. It is concluded that the numerical method can successfully capture the crack paths and accurately predict the fracture behavior of concrete structures. The influence of mode-II parameters on the mixed-mode fracture behavior is further investigated to better determine these parameters.

  20. Nurturing Opportunity Identification for Business Sophistication in a Cross-disciplinary Study Environment

    Directory of Open Access Journals (Sweden)

    Karine Oganisjana

    2012-12-01

    Full Text Available Opportunity identification is the key element of the entrepreneurial process; therefore the issue of developing this skill in students is a crucial task in contemporary European education which has recognized entrepreneurship as one of the lifelong learning key competences. The earlier opportunity identification becomes a habitual way of thinking and behavior across a broad range of contexts, the more likely that entrepreneurial disposition will steadily reside in students. In order to nurture opportunity identification in students for making them able to organize sophisticated businesses in the future, certain demands ought to be put forward as well to the teacher – the person who is to promote these qualities in their students. The paper reflects some findings of a research conducted within the frameworks of a workplace learning project for the teachers of one of Riga secondary schools (Latvia. The main goal of the project was to teach the teachers to identify hidden inner links between apparently unrelated things, phenomena and events within 10th grade study curriculum and connect them together and create new opportunities. The creation and solution of cross-disciplinary tasks were the means for achieving this goal.

  1. Ranking network of a captive rhesus macaque society: a sophisticated corporative kingdom.

    Science.gov (United States)

    Fushing, Hsieh; McAssey, Michael P; Beisner, Brianne; McCowan, Brenda

    2011-03-15

    We develop a three-step computing approach to explore a hierarchical ranking network for a society of captive rhesus macaques. The computed network is sufficiently informative to address the question: Is the ranking network for a rhesus macaque society more like a kingdom or a corporation? Our computations are based on a three-step approach. These steps are devised to deal with the tremendous challenges stemming from the transitivity of dominance as a necessary constraint on the ranking relations among all individual macaques, and the very high sampling heterogeneity in the behavioral conflict data. The first step simultaneously infers the ranking potentials among all network members, which requires accommodation of heterogeneous measurement error inherent in behavioral data. Our second step estimates the social rank for all individuals by minimizing the network-wide errors in the ranking potentials. The third step provides a way to compute confidence bounds for selected empirical features in the social ranking. We apply this approach to two sets of conflict data pertaining to two captive societies of adult rhesus macaques. The resultant ranking network for each society is found to be a sophisticated mixture of both a kingdom and a corporation. Also, for validation purposes, we reanalyze conflict data from twenty longhorn sheep and demonstrate that our three-step approach is capable of correctly computing a ranking network by eliminating all ranking error.

  2. Ranking network of a captive rhesus macaque society: a sophisticated corporative kingdom.

    Directory of Open Access Journals (Sweden)

    Hsieh Fushing

    2011-03-01

    Full Text Available We develop a three-step computing approach to explore a hierarchical ranking network for a society of captive rhesus macaques. The computed network is sufficiently informative to address the question: Is the ranking network for a rhesus macaque society more like a kingdom or a corporation? Our computations are based on a three-step approach. These steps are devised to deal with the tremendous challenges stemming from the transitivity of dominance as a necessary constraint on the ranking relations among all individual macaques, and the very high sampling heterogeneity in the behavioral conflict data. The first step simultaneously infers the ranking potentials among all network members, which requires accommodation of heterogeneous measurement error inherent in behavioral data. Our second step estimates the social rank for all individuals by minimizing the network-wide errors in the ranking potentials. The third step provides a way to compute confidence bounds for selected empirical features in the social ranking. We apply this approach to two sets of conflict data pertaining to two captive societies of adult rhesus macaques. The resultant ranking network for each society is found to be a sophisticated mixture of both a kingdom and a corporation. Also, for validation purposes, we reanalyze conflict data from twenty longhorn sheep and demonstrate that our three-step approach is capable of correctly computing a ranking network by eliminating all ranking error.

  3. The chloroplast thylakoid membrane system is a molecular conveyor belt.

    Science.gov (United States)

    Critchley, C

    1988-10-01

    Light drives photosynthesis, but paradoxically light is also the most variable environmental factor influencing photosynthesis both qualitatively and quantitatively. The photosynthetic apparatus of higher plants is adaptable in the extreme, as exemplified by its capacity for acclimation to very bright sunny or deeply shaded conditions. It can also respond to rapid changes in light such as sunflecks. In this paper I offer a model that i) explains the thylakoid membrane organisation into grana stacks and stroma lamellae, ii) proposes a role for rapid D1 protein turnover and LHCII phosphorylation, and iii) suggests a mechanism for photoinhibition. I argue that the photosynthetic membrane system is dynamic in three dimensions, so much so that, in the light, it is in constant motion and operates in a manner somewhat analogous to a conveyor belt. D1 protein degradation is proposed to be the motor that drives this system. Photoinhibition is suggested to be due to the arrest of D1 protein turnover.

  4. Molecular pathology of systemic lupus erythematosus in Asians

    OpenAIRE

    Chai, Hwa Chia

    2017-01-01

    Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease affecting various parts of the body. Polymorphisms in genes involved in toll-like receptor (TLR)/interferon (IFN) signalling pathways have been reported previously to be associated with SLE in many populations. This study aimed to investigate the role of seven single nucleotide polymorphisms (SNPs) within TNFAIP3 (rs2230936 and rs3757173), STAT4 (rs7574865, rs10168266, and rs7601754), and IRF5 (rs4728142 and rs729302), that...

  5. Bound states and molecular structure of systems with hyperons

    International Nuclear Information System (INIS)

    Akaishi, Y.

    1992-01-01

    Microscopic calculations are done for Σ-hypernuclear few-body systems by a method named ATMS. Among two- to five-body systems, only the Σ 4 He(0 + ) and Σ 4 H(0 + ) hypernuclei are expected to be bound: The binding energy and the width of the former are calculated to be 3.7 ∼ 4.6 MeV and 4.5 ∼ 7.9 MeV, respectively. The observation of Σ 4 He at KEK is in good agreement with the above prediction. The nucleus-Σ potential has a strong Lane term and a repulsive bump at short distance. The Lane term makes the system bound and the bump suppresses the ΣN → ΛN conversion. X-ray measurement of level shifts in the 4 He-Σ - , 3 He-Σ - and 3 H-Σ - atoms can provide another information on the Lane term. In 208 Pb, there may exist a peculiar state, Coulomb-assisted (atomnucleus) hybrid state, where Σ - is trapped in the surface region by the strong interaction with the aid of the inner centrifugal repulsion and the outer Coulomb attraction. An analysis is given for new data of Ξ -.12 C atomic or nuclear systems from the emulsion-counter experiment at KEK. The double-Λ hypernucleus formation rate is calculated for a stopped Ξ - on 4 He. A high branching ratio of 37% is obtained for the ΛΛ 4 H formation from a Ξ -.4 He atom. The detection of about 2.3 MeV neutron is proposed to search for lightest double-Λ hypernucleus ΛΛ 4 H. (author)

  6. Biomedical wellness monitoring system based upon molecular markers

    Science.gov (United States)

    Ingram, Whitney

    2012-06-01

    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  7. Molecular dynamics and diffusion a compilation

    CERN Document Server

    Fisher, David

    2013-01-01

    The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

  8. Supra-molecular Association and Polymorphic Behaviour In Systems Containing Bile Acid Salts

    Directory of Open Access Journals (Sweden)

    Camillo La Mesa

    2007-08-01

    Full Text Available A wide number of supra-molecular association modes are observed in mixtures containing water and bile salts, BS, (with, eventually, other components. Molecular or micellar solutions transform into hydrated solids, fibres, lyotropic liquid crystals and/or gels by raising the concentration, the temperature, adding electrolytes, surfactants, lipids and proteins. Amorphous or ordered phases may be formed accordingly. The forces responsible for this very rich polymorphism presumably arise from the unusual combination of electrostatic, hydrophobic and hydrogen-bond contributions to the system stability, with subsequent control of the supra-molecular organisation modes. The stabilising effect due to hydrogen bonds does not occur in almost all surfactants or lipids and is peculiar to bile acids and salts. Some supra-molecular organisation modes, supposed to be related to malfunctions and dis-metabolic diseases in vivo, are briefly reported and discussed.

  9. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

    Science.gov (United States)

    Muto, Yutaka; Yokoyama, Shigeyuki

    2012-01-01

    'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

  10. Molecular alteration of a muscarinic acetylcholine receptor system during synaptogenesis

    International Nuclear Information System (INIS)

    Large, T.H.; Cho, N.J.; De Mello, F.G.; Klein, W.L.

    1985-01-01

    Biochemical properties of the muscarinic acetylcholine receptor system of the avian retina were found to change during the period when synapses form in ovo. Comparison of ligand binding to membranes obtained before and after synaptogenesis showed a significant increase in the affinity, but not proportion, of the high affinity agonist-binding state. There was no change in receptor sensitivity to antagonists during this period. Pirenzepine binding, which can discriminate muscarinic receptor subtypes, showed the presence of a single population of low affinity sites (M2) before and after synaptogenesis. The change in agonist binding was not due to the late development of receptor function. However, detergent-solubilization of membranes eliminated differences in agonist binding between receptors from embryos and hatched chicks, suggesting a developmental change in interactions of the receptor with functionally related membrane components. A possible basis for altered interactions was obtained from isoelectric point data showing that the muscarinic receptor population underwent a transition from a predominantly low pI form (4.25) in 13 day embryos to a predominantly high pI form (4.50) in newly hatched chicks. The possibility that biochemical changes in the muscarinic receptor play a role in differentiation of the system by controlling receptor position on the surface of nerve cells is discussed

  11. Chapter 5: Quantum Dynamics in Dissipative Molecular Systems

    Science.gov (United States)

    Zhang, Hou-Dao; Xu, J.; Xu, Rui-Xue; Yan, Y. J.

    2014-04-01

    The following sections are included: * Introduction * HEOM versus Path Integral Formalism: Background * Generic form and terminology of HEOM * Statistical mechanics description of bath influence * Feynman-Vernon influence functional formalism * General comments * Memory-Frequency Decomposition of Bath Correlation Functions * PSD of Bose function * Brownian oscillators decomposition of bath spectral density function * Optimized HEOM Theory With Accuracy Control * Construction of HEOM via path integral formalism * Accuracy control on white-noise residue ansatz * Efficient HEOM propagator: Numerical filtering and indexing algorithm * HEOM in Quantum Mechanics for Open Systems * The HEOM space and the Schrödinger picture * HEOM in the Heisenberg picture * Mixed Heisenberg-Schrödinger block-matrix dynamics in nonlinear optical response functions * Two-Dimensional Spectroscopy: Model Calculations * Concluding Remarks * Acknowledgments * References

  12. Intracellular Chemistry: Integrating Molecular Inorganic Catalysts with Living Systems.

    Science.gov (United States)

    Ngo, Anh H; Bose, Sohini; Do, Loi H

    2018-03-23

    This concept article focuses on the rapid growth of intracellular chemistry dedicated to the integration of small-molecule metal catalysts with living cells and organisms. Although biological systems contain a plethora of biomolecules that can deactivate inorganic species, researchers have shown that small-molecule metal catalysts could be engineered to operate in heterogeneous aqueous environments. Synthetic intracellular reactions have recently been reported for olefin hydrogenation, hydrolysis/oxidative cleavage, azide-alkyne cycloaddition, allylcarbamate cleavage, C-C bond cross coupling, and transfer hydrogenation. Other promising targets for new biocompatible reaction discovery will also be discussed, with a special emphasis on how such innovations could lead to the development of novel technologies and chemical tools. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Molecular dynamics coupled with a virtual system for effective conformational sampling.

    Science.gov (United States)

    Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

    2018-07-15

    An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  14. Phases of polymer systems in solution studied via molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Joshua Allen [Iowa State Univ., Ames, IA (United States)

    2009-05-01

    Polymers are amazingly versatile molecules with a tremendous range of applications. Our lives would be very different without them. There would be no multitudes of plastic encased electronic gizmos, no latex paint on the walls and no rubber tires, just to name a few of the many commonplace polymer materials. In fact, life as we know it wouldn’t exist without polymers as two of the most essential types of molecules central to cellular life, Proteins and DNA, are both polymers! [1] With their wide range of application to a variety of uses, polymers are still a very active field in basic research. Of particular current interest is the idea of combining polymers with inorganic particles to form novel composite materials. [2] As computers are becoming faster, they are becoming all the more powerful tools for modeling and simulating real systems. With recent advances in computing on graphics processing units (GPUs) [3–7], questions can now be answered via simulation that could not even be asked before. This thesis focuses on the use of computer simulations to model novel polymerinorganic composite systems in order to predict what possible phases can form and under what conditions. The goal is to provide some direction for future experiments and to gain a deeper understanding of the fundamental physics involved. Along the way, there are some interesting and essential side-tracks in the areas of equilibrating complicated phases and accelerating the available computer power with GPU computing, both of which are necessary steps to enable the study of polymer nanocomposites.

  15. Modulated molecular beam mass spectrometry: A generalized expression for the ''reaction product vector'' for linear systems

    International Nuclear Information System (INIS)

    Chang, H.; Weinberg, W.H.

    1977-01-01

    A generalized expression is developed that relates the ''reaction product vector'', epsilon exp(-iphi), to the kinetic parameters of a linear system. The formalism is appropriate for the analysis of modulated molecular beam mass spectrometry data and facilitates the correlation of experimental results to (proposed) linear models. A study of stability criteria appropriate for modulated molecular beam mass spectrometry experiments is also presented. This investigation has led to interesting inherent limitations which have not heretofore been emphasized, as well as a delineation of the conditions under which stable chemical oscillations may occur in the reacting system

  16. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    International Nuclear Information System (INIS)

    Czaja, MaIgorzata; Baginska, Katarzyna; Kozak, Anna; Makowski, Mariusz; Chmurzynski, Lech

    2005-01-01

    Molecular heteroconjugation constants, K BHA DMSO and K AHB DMSO , expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK a DMSO (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK BHA DMSO values and pK a DMSO (HA). Furthermore, overall stability constants, lgK o DMSO , could be correlated linearly with pK a DMSO (HA) values

  17. Low molecular mass chitosan as carrier for hydrodynamically balanced system for sustained delivery of ciprofloxacin hydrochloride

    OpenAIRE

    VERMA, ANURAG; BANSAL, ASHOK K.; GHOSH, AMITAVA; PANDIT, JAYANTA K.

    2012-01-01

    Chitosan has become a focus of major interest in recent years due to its excellent biocompatibility, biodegradability and non-toxicity. Although this material has already been extensively investigated in the design of different types of drug delivery systems, it is still little explored for stomach specific drug delivery systems. The objective of the present investigation was to explore the potential of low molecular mass chitosan (LMCH) as carrier for a hydrodynamically balanced system (HBS)...

  18. Sophisticated Online Learning Scheme for Green Resource Allocation in 5G Heterogeneous Cloud Radio Access Networks

    KAUST Repository

    Alqerm, Ismail

    2018-01-23

    5G is the upcoming evolution for the current cellular networks that aims at satisfying the future demand for data services. Heterogeneous cloud radio access networks (H-CRANs) are envisioned as a new trend of 5G that exploits the advantages of heterogeneous and cloud radio access networks to enhance spectral and energy efficiency. Remote radio heads (RRHs) are small cells utilized to provide high data rates for users with high quality of service (QoS) requirements, while high power macro base station (BS) is deployed for coverage maintenance and low QoS users service. Inter-tier interference between macro BSs and RRHs and energy efficiency are critical challenges that accompany resource allocation in H-CRANs. Therefore, we propose an efficient resource allocation scheme using online learning, which mitigates interference and maximizes energy efficiency while maintaining QoS requirements for all users. The resource allocation includes resource blocks (RBs) and power. The proposed scheme is implemented using two approaches: centralized, where the resource allocation is processed at a controller integrated with the baseband processing unit and decentralized, where macro BSs cooperate to achieve optimal resource allocation strategy. To foster the performance of such sophisticated scheme with a model free learning, we consider users\\' priority in RB allocation and compact state representation learning methodology to improve the speed of convergence and account for the curse of dimensionality during the learning process. The proposed scheme including both approaches is implemented using software defined radios testbed. The obtained results and simulation results confirm that the proposed resource allocation solution in H-CRANs increases the energy efficiency significantly and maintains users\\' QoS.

  19. Molecular evolution of peptidergic signaling systems in bilaterians

    Science.gov (United States)

    Mirabeau, Olivier; Joly, Jean-Stéphane

    2013-01-01

    Peptide hormones and their receptors are widespread in metazoans, but the knowledge we have of their evolutionary relationships remains unclear. Recently, accumulating genome sequences from many different species have offered the opportunity to reassess the relationships between protostomian and deuterostomian peptidergic systems (PSs). Here we used sequences of all human rhodopsin and secretin-type G protein-coupled receptors as bait to retrieve potential homologs in the genomes of 15 bilaterian species, including nonchordate deuterostomian and lophotrochozoan species. Our phylogenetic analysis of these receptors revealed 29 well-supported subtrees containing mixed sets of protostomian and deuterostomian sequences. This indicated that many vertebrate and arthropod PSs that were previously thought to be phyla specific are in fact of bilaterian origin. By screening sequence databases for potential peptides, we then reconstructed entire bilaterian peptide families and showed that protostomian and deuterostomian peptides that are ligands of orthologous receptors displayed some similarity at the level of their primary sequence, suggesting an ancient coevolution between peptide and receptor genes. In addition to shedding light on the function of human G protein-coupled receptor PSs, this work presents orthology markers to study ancestral neuron types that were probably present in the last common bilaterian ancestor. PMID:23671109

  20. Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments.

    Directory of Open Access Journals (Sweden)

    Tihamér Geyer

    Full Text Available Metabolic processes in biological cells are commonly either characterized at the level of individual enzymes and metabolites or at the network level. Often these two paradigms are considered as mutually exclusive because concepts from neither side are suited to describe the complete range of scales. Additionally, when modeling metabolic or regulatory cellular systems, often a large fraction of the required kinetic parameters are unknown. This even applies to such simple and extensively studied systems like the photosynthetic apparatus of purple bacteria. Using the chromatophore vesicles of Rhodobacter sphaeroides as a model system, we show that a consistent kinetic model emerges when fitting the dynamics of a molecular stochastic simulation to a set of time dependent experiments even though about two thirds of the kinetic parameters in this system are not known from experiment. Those kinetic parameters that were previously known all came out in the expected range. The simulation model was built from independent protein units composed of elementary reactions processing single metabolites. This pools-and-proteins approach naturally compiles the wealth of available molecular biological data into a systemic model and can easily be extended to describe other systems by adding new protein or nucleic acid types. The automated parameter optimization, performed with an evolutionary algorithm, reveals the sensitivity of the model to the value of each parameter and the relative importances of the experiments used. Such an analysis identifies the crucial system parameters and guides the setup of new experiments that would add most knowledge for a systemic understanding of cellular compartments. The successful combination of the molecular model and the systemic parametrization presented here on the example of the simple machinery for bacterial photosynthesis shows that it is actually possible to combine molecular and systemic modeling. This framework can now

  1. Building Models in the Classroom: Taking Advantage of Sophisticated Geomorphic Numerical Tools Using a Simple Graphical User Interface

    Science.gov (United States)

    Roy, S. G.; Koons, P. O.; Gerbi, C. C.; Capps, D. K.; Tucker, G. E.; Rogers, Z. A.

    2014-12-01

    Sophisticated numerical tools exist for modeling geomorphic processes and linking them to tectonic and climatic systems, but they are often seen as inaccessible for users with an exploratory level of interest. We have improved the accessibility of landscape evolution models by producing a simple graphics user interface (GUI) that takes advantage of the Channel-Hillslope Integrated Landscape Development (CHILD) model. Model access is flexible: the user can edit values for basic geomorphic, tectonic, and climate parameters, or obtain greater control by defining the spatiotemporal distributions of those parameters. Users can make educated predictions by choosing their own parametric values for the governing equations and interpreting the results immediately through model graphics. This method of modeling allows users to iteratively build their understanding through experimentation. Use of this GUI is intended for inquiry and discovery-based learning activities. We discuss a number of examples of how the GUI can be used at the upper high school, introductory university, and advanced university level. Effective teaching modules initially focus on an inquiry-based example guided by the instructor. As students become familiar with the GUI and the CHILD model, the class can shift to more student-centered exploration and experimentation. To make model interpretations more robust, digital elevation models can be imported and direct comparisons can be made between CHILD model results and natural topography. The GUI is available online through the University of Maine's Earth and Climate Sciences website, through the Community Surface Dynamics Modeling System (CSDMS) model repository, or by contacting the corresponding author.

  2. Coherent Rabi oscillations in a molecular system and sub-diffraction-limited pattern generation

    International Nuclear Information System (INIS)

    Liao, Zeyang; Al-Amri, M; Zubairy, M Suhail

    2015-01-01

    The resolution of a photolithography and optical imaging system is restricted by the diffraction limit. Coherent Rabi oscillations have been shown to be able to overcome the diffraction limit in a simple two-level atomic system (Z Liao, M Al-amri, and M S Zubairy 2010 Phys. Rev. Lett. 105 183601). In this paper, we numerically calculate the wave packet dynamics of a molecular system interacting with an ultrashort laser pulse and show that coherent Rabi oscillations in a molecular system are also possible. Moreover, a sub-diffraction-limited pattern can be generated in this system by introducing spatially modulated Rabi oscillations. We also discuss several techniques to improve the visibility of the sub-diffraction-limited pattern. Our result may have important applications in super-resolution optical lithography and optical imaging. (paper)

  3. A neural network approach to the study of dynamics and structure of molecular systems

    International Nuclear Information System (INIS)

    Getino, C.; Sumpter, B.G.; Noid, D.W.

    1994-01-01

    Neural networks are used to study intramolecular energy flow in molecular systems (tetratomics to macromolecules), developing new techniques for efficient analysis of data obtained from molecular-dynamics and quantum mechanics calculations. Neural networks can map phase space points to intramolecular vibrational energies along a classical trajectory (example of complicated coordinate transformation), producing reasonably accurate values for any region of the multidimensional phase space of a tetratomic molecule. Neural network energy flow predictions are found to significantly enhance the molecular-dynamics method to longer time-scales and extensive averaging of trajectories for macromolecular systems. Pattern recognition abilities of neural networks can be used to discern phase space features. Neural networks can also expand model calculations by interpolation of costly quantum mechanical ab initio data, used to develop semiempirical potential energy functions

  4. Large-scale molecular dynamics simulations of self-assembling systems.

    Science.gov (United States)

    Klein, Michael L; Shinoda, Wataru

    2008-08-08

    Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.

  5. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    Science.gov (United States)

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  6. Molecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcers

    NARCIS (Netherlands)

    Bos, C. L.; van Baarsen, L. G. M.; Timmer, T. C. G.; Overbeek, M. J.; Basoski, N. M.; Rustenburg, F.; Baggen, J. M. C.; Thiesen, H. J.; Dijkmans, B. A. C.; van der Pouw Kraan, T. C. T. M.; Voskuyl, A. E.; Verweij, C. L.

    2009-01-01

    The objective of this study was to identify molecular profiles that may distinguish clinical subtypes in systemic sclerosis (SSc). Large-scale gene expression profiling was performed on peripheral blood (PB) from 12 SSc patients and 6 healthy individuals. Significance analysis of microarrays,

  7. On the effects of transforming the vibrational spectra of molecular systems under microwave radiation

    International Nuclear Information System (INIS)

    Serikov, A.A.

    1993-01-01

    This problem is analyzed within the quantum-classical theory of molecular spectra. It is shown that the above-mentioned spectrum transformation could be, in principle, realized in macromolecular systems with strong interaction, and attention is drawn to the resonance character of the effect. (author). 19 refs., 1 fig

  8. Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

    Science.gov (United States)

    Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin

    2016-01-20

    The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

  9. Structure and properties of simple molecular systems at very high density

    International Nuclear Information System (INIS)

    LeSar, R.

    1989-01-01

    The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

  10. Development of Optical Molecular Imaging System for the Acquisition of Bioluminescence Signals from Small Animals

    International Nuclear Information System (INIS)

    Lee, Byeong Il; Kim, Hyeon Sik; Jeong, Hye Jin; Lee, Hyung Jae; Moon, Seung Min; Kwon, Seung Young; Jeong, Shin Young; Bom, Hee Seung; Min, Jung Joon; Choi, Eun Seo

    2009-01-01

    Optical imaging is providing great advance and improvement in genetic and molecular imaging of animals and humans. Optical imaging system consists of optical imaging devices, which carry out major function for monitoring, tracing, and imaging in most of molecular in-vivo researches. In bio-luminescent imaging, small animals containing luciferase gene locally irradiate light, and emitted photons transmitted through skin of the small animals are imaged by using a high sensitive charged coupled device (CCD) camera. In this paper, we introduced optical imaging system for the image acquisition of bio-luminescent signals emitted from small animals. In the system, Nikon lens and four LED light sources were mounted at the inside of a dark box. A cooled CCD camera equipped with a control module was used. We tested the performance of the optical imaging system using effendorf tube and light emitting bacteria which injected intravenously into CT26 tumor bearing nude mouse. The performance of implemented optical imaging system for bio-luminescence imaging was demonstrated and the feasibility of the system in small animal imaging application was proved. We anticipate this system could be a useful tool for the molecular imaging of small animals adaptable for various experimental conditions in future

  11. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  12. Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

    Directory of Open Access Journals (Sweden)

    Miguel Fribourg

    2017-02-01

    Full Text Available Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic processes from the overall (macroscopic response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE. SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology

  13. Studies of isotopic effects in the excited electronic states of molecular systems

    International Nuclear Information System (INIS)

    1982-01-01

    Rare gas halogen (RGH) lasers serve as convenient tools for a range of photophysical processes which exhibit isotope effects. This document summarizes progress in the production of molecular systems in their electronic excited states with the aid of RGH lasers, and the various isotopic effects one can study under these conditions. We conclude that the basic physical mechanisms involved in the isotopically sensitive characteristics of excited molecular electronic states are sufficiently selective to be useful in both the detection and separation of many atomic materials

  14. Advanced in study of cellular and molecular mechanisms of radiation effects on central nervous system

    International Nuclear Information System (INIS)

    Zhang Wei; Tu Yu; Wang Lili

    2008-01-01

    Along with radiation treatment extensively applied, radiation injury also is valued gradually. The effect of radiation to the cellular and molecular of central nervous system (CNS) is a complicated and moderately advanced process and the mechanism is remains incompletely clear yet. Inquiring into the possible mechanism of the CNS including the injury and the restoration of neuron, neuroglia cells, endotheliocyte cell and blood-brain barrier and the molecular level of change induced by radiation, so as to provide beneficial thought for preventing and curing radiation injury clinically. Some neuroprotective strategies are also addressed in the review. (authors)

  15. Sophisticated Approval Voting, Ignorance Priors, and Plurality Heuristics: A Behavioral Social Choice Analysis in a Thurstonian Framework

    Science.gov (United States)

    Regenwetter, Michel; Ho, Moon-Ho R.; Tsetlin, Ilia

    2007-01-01

    This project reconciles historically distinct paradigms at the interface between individual and social choice theory, as well as between rational and behavioral decision theory. The authors combine a utility-maximizing prescriptive rule for sophisticated approval voting with the ignorance prior heuristic from behavioral decision research and two…

  16. Purification through Emotions: The Role of Shame in Plato's "Sophist" 230B4-E5

    Science.gov (United States)

    Candiotto, Laura

    2018-01-01

    This article proposes an analysis of Plato's "Sophist" (230b4--e5) that underlines the bond between the logical and the emotional components of the Socratic "elenchus", with the aim of depicting the social valence of this philosophical practice. The use of emotions characterizing the 'elenctic' method described by Plato is…

  17. Energy transformation in molecular electronic systems: Comprehensive progress report, 1986--1989

    International Nuclear Information System (INIS)

    Kasha, M.

    1989-01-01

    Our research focuses on discovering the fundamental issues in proton-transfer and charge-transfer excitations in model systems, with an eye on which molecular systems will serve as the best guide to biological systems. This report addresses an intramolecular proton transfer classification system, proton-transfer potentials, proton-transfer spectroscopy of benzanilides, proton-transfer in aminosalicylates, proton-transfer in lumichrome, development of proton-transfer lasers, and triplet excitation enhancement via proton-transfer tunneling. 6 refs., 2 figs

  18. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    Energy Technology Data Exchange (ETDEWEB)

    Li, King C.P. [Department of Radiology, Methodist Hospital, Weill Cornell Medical College, 6565 Fannin Street, D280 Houston, TX 77030 (United States)], E-mail: kli@tmhs.org

    2009-05-15

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  19. Dynamic analysis of electron density in the course of the internal motion of molecular system

    International Nuclear Information System (INIS)

    Tachibana, A.; Hori, K.; Asai, Y.; Yamabe, T.

    1984-01-01

    The general dynamic aspect of electron density of a molecular system is studied on the basis of the general equation of the electron orbital which is formulated for the dynamic study of electronic motion. The newly defined electron orbital incorporates the dynamics of molecular vibration into the electronic structures. In this scheme, the change of electron distribution caused by excitation of vibrational state is defined as the ''dynamic electron transfer.'' The dynamic electron density is found to have the remarkable ''additive'' property. The time-dependent aspect of the dynamic electron redistribution is also analyzed on the basis of the ''coherent state.'' The new method relates the classical vibrational amplitude to the quantum number of the vibrational state. As a preliminary application of the present treatment, the dynamic electron densities of H 2 , HD, HT, HF, and HCl molecules are calculated by use of ab initio molecular orbital method

  20. Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

    Science.gov (United States)

    Kulasiri, Don

    2011-01-01

    We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

  1. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

    Science.gov (United States)

    Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

    2014-06-14

    Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

  2. An analytic approach to 2D electronic PE spectra of molecular systems

    International Nuclear Information System (INIS)

    Szoecs, V.

    2011-01-01

    Graphical abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems using direct calculation from electronic Hamiltonians allows peak classification from 3P-PE spectra dynamics. Display Omitted Highlights: → RWA approach to electronic photon echo. → A straightforward calculation of 2D electronic spectrograms in finite molecular systems. → Importance of population time dynamics in relation to inter-site coherent coupling. - Abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems and simplified line broadening models is presented. The Fourier picture of a heterodyne detected three-pulse rephasing PE signal in the δ-pulse limit of the external field is derived in analytic form. The method includes contributions of one and two-excitonic states and allows direct calculation of Fourier PE spectrogram from corresponding Hamiltonian. As an illustration, the proposed treatment is applied to simple systems, e.g. 2-site two-level system (TLS) and n-site TLS model of photosynthetic unit. The importance of relation between Fourier picture of 3P-PE dynamics (corresponding to nonzero population time, T) and coherent inter-state coupling is emphasized.

  3. Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems

    International Nuclear Information System (INIS)

    Deumens, E.; Diz, A.; Longo, R.; Oehrn, Y.

    1994-01-01

    An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems. The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the ab initio Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecular systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed

  4. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

    Directory of Open Access Journals (Sweden)

    Sophie S Abby

    Full Text Available Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher. It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles is distributed as a compressed tarball archive as Supporting Information.

  5. Introducing Stable Radicals into Molecular Machines.

    Science.gov (United States)

    Wang, Yuping; Frasconi, Marco; Stoddart, J Fraser

    2017-09-27

    Ever since their discovery, stable organic radicals have received considerable attention from chemists because of their unique optical, electronic, and magnetic properties. Currently, one of the most appealing challenges for the chemical community is to develop sophisticated artificial molecular machines that can do work by consuming external energy, after the manner of motor proteins. In this context, radical-pairing interactions are important in addressing the challenge: they not only provide supramolecular assistance in the synthesis of molecular machines but also open the door to developing multifunctional systems relying on the various properties of the radical species. In this Outlook, by taking the radical cationic state of 1,1'-dialkyl-4,4'-bipyridinium (BIPY •+ ) as an example, we highlight our research on the art and science of introducing radical-pairing interactions into functional systems, from prototypical molecular switches to complex molecular machines, followed by a discussion of the (i) limitations of the current systems and (ii) future research directions for designing BIPY •+ -based molecular machines with useful functions.

  6. [Motivation and Emotional States: Structural Systemic, Neurochemical, Molecular and Cellular Mechanisms].

    Science.gov (United States)

    Bazyan, A S

    2016-01-01

    The structural, systemic, neurochemical, molecular and cellular mechanisms of organization and coding motivation and emotional states are describe. The GABA and glutamatergic synaptic systems of basal ganglia form a neural network and participate in the implementation of voluntary behavior. Neuropeptides, neurohormones and paracrine neuromodulators involved in the organization of motivation and emotional states, integrated with synaptic systems, controlled by neural networks and organizing goal-directed behavior. Structural centers for united and integrated of information in voluntary and goal-directed behavior are globus pallidus. Substantia nigra pars reticulata switches the information from corticobasal networks to thalamocortical networks, induces global dopaminergic (DA) signal and organize interaction of mesolimbic and nigostriatnoy DA systems controlled by prefrontal and motor cortex. Together with the motor cortex, substantia nigra displays information in the brainstem and spinal cord to implementation of behavior. Motivation states are formed in the interaction of neurohormonal and neuropeptide systems by monoaminergic systems of brain. Emotional states are formed by monoaminergic systems of the mid-brain, where the leading role belongs to the mesolimbic DA system. The emotional and motivation state of the encoded specific epigenetic molecular and chemical pattern of neuron.

  7. A molecular beam/quadrupole mass spectrometer system with synchronized beam modulation and digital waveform analysis

    Science.gov (United States)

    Pellett, G. L.; Adams, B. R.

    1983-01-01

    A performance evaluation is conducted for a molecular beam/mass spectrometer (MB/MS) system, as applied to a 1-30 torr microwave-discharge flow reactor (MWFR) used in the formation of the methylperoxy radical and a study of its subsequent destruction in the presence or absence of NO(x). The modulated MB/MS system is four-staged and differentially pumped. The results obtained by the MWFR study is illustrative of overall system performance, including digital waveform analysis; significant improvements over previous designs are noted in attainable S/N ratio, detection limit, and accuracy.

  8. Radiopharmaceuticals: nanoparticles like multi-functional systems for the obtaining in vivo of molecular images

    International Nuclear Information System (INIS)

    Ferro F, G.; Ramirez de la Cruz, F. M.; Ocampo G, B. E.; Morales A, E.; Santos C, C. L.; Mendoza S, A. N.

    2010-01-01

    The techniques of obtaining direct or indirect molecular images detect and register the space-temporary distribution of molecular or cellular processes for biochemical, biological, diagnostic and therapeutic applications. The advanced techniques of image like the nuclear magnetic resonance, the single photon emission computed tomography, the positron emission tomography and the images of optic fluorescence have been used successfully to detect these processes. On the other hand, the utility of the nanoparticles for any application is dependent of the physicochemical properties that present, being possible to modify their surface when making them react with different biomolecules what allows the formation of conjugates with specific molecular recognition. The joint of various protein molecules, peptides or oligonucleotides to the surface of a nanoparticle produce a multi-functional system able to increase the multivalent joints from the nanoparticles-biomolecules to their receivers for the obtaining of molecular images in vivo. The peptides stimulate, regulate or inhibit numerous functions of the life, acting mainly as information transmitters and activity coordinators of several tissues in the organism. The receivers of regulator peptides are over represented in numerous types of cancer cells and they are protein structures. These receivers have been used as white molecular of marked peptides, to locate primary malignant tumors and their metastasis, using the diagnostic techniques of molecular image mentioned above, which consist basically on the radio peptides use and conjugated peptides to fluoro chromes, to metallic nanoparticles and nano crystals. A summary of the work is presented carried out by the personnel of the Radio-active Materials and Chemistry Departments of the Instituto Nacional de Investigaciones Nucleares in this field. (Author)

  9. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    Energy Technology Data Exchange (ETDEWEB)

    Czaja, MaIgorzata [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Baginska, Katarzyna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Kozak, Anna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Makowski, Mariusz [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Chmurzynski, Lech [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland)]. E-mail: lech@chem.univ.gda.pl

    2005-08-15

    Molecular heteroconjugation constants, K{sub BHA}{sup DMSO} and K{sub AHB}{sup DMSO}, expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK{sub a}{sup DMSO} (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK{sub BHA}{sup DMSO} values and pK{sub a}{sup DMSO} (HA). Furthermore, overall stability constants, lgK{sub o}{sup DMSO}, could be correlated linearly with pK{sub a}{sup DMSO} (HA) values.

  10. On the molecular anisotropy of liquid crystalline and flexible polymer systems

    Science.gov (United States)

    van Horn, Brett L.

    The demand for products of ever increasing quality or for novel applications has required increasing attention to or manipulation of the anisotropy of manufactured parts. Oriented plastics are used everywhere from recording film to automotive body parts to monofilament fishing line. Liquid crystals are also used in a wide array of applications including their dominance in the flat panel display industry, color changing temperature sensors, and woven bullet resistant fabrics. Anisotropy can also be detrimental, for instance sometimes leading to poor fracture resistance or low yield stress along specific directions. Controlling and measuring anisotropy of materials has become increasingly important, but doing so is wrought with challenges. Measuring physical properties of isotropic liquids, such as water or most oils can be done in a straightforward fashion. Their viscosities and densities, for example, have unique values under a given set of conditions. With anisotropic fluids, like liquid crystals, the viscosity, for instance, will not only depend upon temperature, concentration, etc. but also upon the direction of observation, degree of anisotropy, source of anisotropy, and so forth. This added degree of complexity complicates our ability to define the state of the material at which the measurements are made and generally necessitates the use of more sophisticated measurement strategies or techniques. This work presents techniques and tools for investigating anisotropy in liquid crystalline and stretched polymeric systems. Included are the use of conoscopy for the determination of birefringence and orientation of nematic liquid crystals and stretched polymers, the shear response of flow aligning nematic liquid crystal monodomains, and the design of a novel linear rheometer that allows for in situ optical or scattering investigations.

  11. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

    Science.gov (United States)

    Wen, Fuyu; Li, Can

    2013-11-19

    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  12. Quantitative computational models of molecular self-assembly in systems biology.

    Science.gov (United States)

    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.

  13. A Pilot-Scale System for Carbon Molecular Sieve Hollow Fiber Membrane Manufacturing

    KAUST Repository

    Karvan, O.

    2012-12-21

    Carbon molecular sieve (CMS) membranes offer advantages over traditional polymeric membrane materials, but scale-up of manufacturing systems has not received much attention. In the recent decade, there has been a dramatic increase in fundamental research on these materials with a variety of applications being studied. The results from a pilot-scale CMS production system are presented. This system was designed based on extensive laboratory research, and hollow fiber membranes produced in this system show similar performance compared to membranes produced using a smaller bench-scale system. After optimizing the system design, a 93% recovery of the precursor fibers for use in membrane module preparation were obtained. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Synthesis of Heteroaromatic Compounds by Oxidative Aromatization Using an Activated Carbon/Molecular Oxygen System

    Directory of Open Access Journals (Sweden)

    Masahiko Hayashi

    2009-08-01

    Full Text Available A variety of heteroaromatic compounds, such as substituted pyridines, pyrazoles, indoles, 2-substituted imidazoles, 2-substituted imidazoles, 2-arylbenzazoles and pyrimidin-2(1H-ones are synthesized by oxidative aromatization using the activated carbon and molecular oxygen system. Mechanistic study focused on the role of activated carbon in the synthesis of 2-arylbenzazoles is also discussed. In the final section, we will disclose the efficient synthesis of substituted 9,10-anthracenes via oxidative aromatization.

  15. AUTOMR: An automatic processing program system for the molecular replacement method

    International Nuclear Information System (INIS)

    Matsuura, Yoshiki

    1991-01-01

    An automatic processing program system of the molecular replacement method AUTMR is presented. The program solves the initial model of the target crystal structure using a homologous molecule as the search model. It processes the structure-factor calculation of the model molecule, the rotation function, the translation function and the rigid-group refinement successively in one computer job. Test calculations were performed for six protein crystals and the structures were solved in all of these cases. (orig.)

  16. Gene expression-based molecular diagnostic system for malignant gliomas is superior to histological diagnosis.

    Science.gov (United States)

    Shirahata, Mitsuaki; Iwao-Koizumi, Kyoko; Saito, Sakae; Ueno, Noriko; Oda, Masashi; Hashimoto, Nobuo; Takahashi, Jun A; Kato, Kikuya

    2007-12-15

    Current morphology-based glioma classification methods do not adequately reflect the complex biology of gliomas, thus limiting their prognostic ability. In this study, we focused on anaplastic oligodendroglioma and glioblastoma, which typically follow distinct clinical courses. Our goal was to construct a clinically useful molecular diagnostic system based on gene expression profiling. The expression of 3,456 genes in 32 patients, 12 and 20 of whom had prognostically distinct anaplastic oligodendroglioma and glioblastoma, respectively, was measured by PCR array. Next to unsupervised methods, we did supervised analysis using a weighted voting algorithm to construct a diagnostic system discriminating anaplastic oligodendroglioma from glioblastoma. The diagnostic accuracy of this system was evaluated by leave-one-out cross-validation. The clinical utility was tested on a microarray-based data set of 50 malignant gliomas from a previous study. Unsupervised analysis showed divergent global gene expression patterns between the two tumor classes. A supervised binary classification model showed 100% (95% confidence interval, 89.4-100%) diagnostic accuracy by leave-one-out cross-validation using 168 diagnostic genes. Applied to a gene expression data set from a previous study, our model correlated better with outcome than histologic diagnosis, and also displayed 96.6% (28 of 29) consistency with the molecular classification scheme used for these histologically controversial gliomas in the original article. Furthermore, we observed that histologically diagnosed glioblastoma samples that shared anaplastic oligodendroglioma molecular characteristics tended to be associated with longer survival. Our molecular diagnostic system showed reproducible clinical utility and prognostic ability superior to traditional histopathologic diagnosis for malignant glioma.

  17. A field-deployable mobile molecular diagnostic system for malaria at the point of need.

    Science.gov (United States)

    Choi, Gihoon; Song, Daniel; Shrestha, Sony; Miao, Jun; Cui, Liwang; Guan, Weihua

    2016-11-01

    In response to the urgent need of a field-deployable and highly sensitive malaria diagnosis, we developed a standalone, "sample-in-answer-out" molecular diagnostic system (AnyMDx) to enable quantitative molecular analysis of blood-borne malaria in low resource areas. The system consists of a durable battery-powered analyzer and a disposable microfluidic compact disc loaded with reagents ready for use. A low power thermal module and a novel fluorescence-sensing module are integrated into the analyzer for real-time monitoring of loop-mediated isothermal nucleic acid amplification (LAMP) of target parasite DNA. With 10 μL of raw blood sample, the AnyMDx system automates the nucleic acid sample preparation and subsequent LAMP and real-time detection. Under laboratory conditions with whole-blood samples spiked with cultured Plasmodium falciparum, we achieved a detection limit of ∼0.6 parasite per μL, much lower than those for the conventional microscopy and rapid diagnostic tests (∼50-100 parasites per μL). The turnaround time from sample to answer is less than 40 minutes. The AnyMDx is user-friendly requiring minimal technological training. The analyzer and the disposable reagent compact discs are cost-effective, making AnyMDx a potential tool for malaria molecular diagnosis under field settings for malaria elimination.

  18. Resolution of identity approximation for the Coulomb term in molecular and periodic systems

    Science.gov (United States)

    Burow, Asbjörn M.; Sierka, Marek; Mohamed, Fawzi

    2009-12-01

    A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 μhartree per atom, for both molecular and periodic systems.

  19. High Molecular Weight Isoforms of Growth Hormone In Cells of the Immune System

    Science.gov (United States)

    Weigent, Douglas A.

    2013-01-01

    A substantial body of research exists to support the idea that cells of the immune system produce growth hormone (GH). However, the structure and mechanism of action of lymphocyte-derived GH continues to remain largely unknown. Here we present the results of Western analysis of whole cell extracts showing that different molecular weight isoforms of GH of approximately 100 kDa, 65 kDa, and 48 kDa can be detected in primary mouse cells of the immune system and in the mouse EL4 cell line. The identity of the 65 kDa and 48 kDa isoforms of GH were confirmed by mass spectrometry. The various isoforms were detected in both enriched T and B spleen cell populations. The large molecular weight isoform appears to reside primarily in the cytoplasm whereas the lower molecular weight 65 kDa and 48 kDa isoforms were detected primarily in the nucleus. These results also suggest that GH isoforms are induced by oxidative stress. In EL4 cells overexpressing GH, the expression of luciferase controlled by a promoter containing the antioxidant response element is increased almost three-fold above control. The data suggest that the induction of isoforms of the GH molecule in cells of the immune system may be an important mechanism of adaptation and/or protection of lymphoid cells under conditions of oxidative stress. PMID:21741628

  20. Molecular machines in living cells. Seibutsu no bunshi kikai to sono system

    Energy Technology Data Exchange (ETDEWEB)

    Osawa, F. (Aichi Inst. of Tech., Nagoya (Japan))

    1992-12-20

    At first, flagellar motors of bacteria are reviewed as a typical example of molecular machines in living cells. A rotational motor is embedded in the cell membrane at the root of the flagellum. The driving power of the rotation is the flow of hydrogen ion from the inside to the outside of the cell. In a normal state of a bacterium, potential difference of about 0.2 V is produced by the ion pump existing in the cell membrane. A molecular motor of sliding motion of muscle attracts the attention on the relation of the input and output of the molecular motor. The mechanism of the smooth motion without fluctuation in the fluctuated environment and the fluctuated input is unknown. Next, the motion of Paramecium is discussed as an example of a system composed of a number of molecular machines. Paramecium moves to a place of a suitable temperature when placed in a water tank with temperature gradient, however, it does not stop the motion at the place of the suitable temperature and increases a probability to change the direction when leaving, that is it takes a method of indirect probabilistic control. 12 refs., 8 figs.

  1. On the theory of frequency-shifted secondary emission of light-harvesting molecular systems

    International Nuclear Information System (INIS)

    Morozov, V.A.

    2001-01-01

    The expressions are obtained for the intensity of the frequency-shifted secondary emission of a chromophore playing the role of a reaction center in the simplest model three-chromophore molecular 'light-harvesting' antenna, which is constructed and oriented in space so that the incident photons coherently excite two of its chromophore pigments. The quantum-field formalism was used, which takes into account the generalized (quantum-electrodynamic) dipole-dipole, as well as radiative and nonradiative dissipative interactions between pigments and the reaction center of the antenna. The special features of the excitation spectrum of the Raman scattering line and the frequency-shifted fluorescence spectrum of the reaction center of the molecular antenna under study are discussed. A comparison of the expressions obtained for the excitation and fluorescence spectra and with the corresponding expressions obtained for a bichromophore molecular system, which differs from a three-chromophore antenna by the absence of one of the pigments, revealed the properties of the mechanism of action of light-harvesting molecular antennas that have not been found earlier. In particular, it is shown that 'the light-harvesting' caused by the collective dissipative interactions of pigments with the reaction center of the antenna can substantially exceed a sum of contributions from separate pigments

  2. An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Vrhovsek, Aleksander; Gereben, Orsolya; Pothoczki, Szilvia; Pusztai, Laszlo [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49 (Hungary); Tomsic, Matija; Jamnik, Andrej [Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1001 Ljubljana (Slovenia); Kohara, Shinji, E-mail: aleksander.vrhovsek@gmail.co [Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2010-10-13

    An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

  3. Net emission coefficient for CO–H2 thermal plasmas with the consideration of molecular systems

    International Nuclear Information System (INIS)

    Billoux, T.; Cressault, Y.; Gleizes, A.

    2015-01-01

    This paper deals with the calculation of net emission coefficients (NECs) for CO–H 2 thermal plasmas. This task required the elaboration of a complete spectroscopic database including atoms and molecules formed by carbon, oxygen and hydrogen elements. We have used a systematic line by line method to calculate all the main radiative contributions which are the atomic and molecular continua, the atomic lines and the molecular (diatomic and polyatomic) lines. The main diatomic electronic systems for CO–H 2 plasmas and the triatomic molecular bands were considered. We present some variations of the net emission coefficient versus temperature, for various pressures and for two relative proportions of the components. The role of the diatomic molecules is important at temperatures lower than 5000 K whereas the net emission coefficient presents an unusual peak at temperature around 1000 K, due to the presence of the CO 2 molecule presenting a strong infrared radiation. Finally, the results show that the NEC slightly depends on the relative proportion of CO and H 2 . - highlights: • We calculate radiative losses from CO–H 2 thermal plasmas. • We use the up-to-date atomic and molecular databases. • The influence of CO 2 molecule is very important at low temperature. • The relative maximum of the net emission coefficient at low temperature is unusual

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

    International Nuclear Information System (INIS)

    Cavillon, F.

    2004-10-01

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

  5. From Molecular Classification to Targeted Therapeutics: The Changing Face of Systemic Therapy in Metastatic Gastroesophageal Cancer

    Directory of Open Access Journals (Sweden)

    Adrian Murphy

    2015-01-01

    Full Text Available Histological classification of adenocarcinoma or squamous cell carcinoma for esophageal cancer or using the Lauren classification for intestinal and diffuse type gastric cancer has limited clinical utility in the management of advanced disease. Germline mutations in E-cadherin (CDH1 or mismatch repair genes (Lynch syndrome were identified many years ago but given their rarity, the identification of these molecular alterations does not substantially impact treatment in the advanced setting. Recent molecular profiling studies of upper GI tumors have added to our knowledge of the underlying biology but have not led to an alternative classification system which can guide clinician’s therapeutic decisions. Recently the Cancer Genome Atlas Research Network has proposed four subtypes of gastric cancer dividing tumors into those positive for Epstein-Barr virus, microsatellite unstable tumors, genomically stable tumors, and tumors with chromosomal instability. Unfortunately to date, many phase III clinical trials involving molecularly targeted agents have failed to meet their survival endpoints due to their use in unselected populations. Future clinical trials should utilize molecular profiling of individual tumors in order to determine the optimal use of targeted therapies in preselected patients.

  6. Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System.

    Science.gov (United States)

    Banjar, Haneen; Adelson, David; Brown, Fred; Chaudhri, Naeem

    2017-01-01

    The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.

  7. Molecular stratification and precision medicine in systemic sclerosis from genomic and proteomic data.

    Science.gov (United States)

    Martyanov, Viktor; Whitfield, Michael L

    2016-01-01

    The goal of this review is to summarize recent advances into the pathogenesis and treatment of systemic sclerosis (SSc) from genomic and proteomic studies. Intrinsic gene expression-driven molecular subtypes of SSc are reproducible across three independent datasets. These subsets are a consistent feature of SSc and are found in multiple end-target tissues, such as skin and esophagus. Intrinsic subsets as well as baseline levels of molecular target pathways are potentially predictive of clinical response to specific therapeutics, based on three recent clinical trials. A gene expression-based biomarker of modified Rodnan skin score, a measure of SSc skin severity, can be used as a surrogate outcome metric and has been validated in a recent trial. Proteome analyses have identified novel biomarkers of SSc that correlate with SSc clinical phenotypes. Integrating intrinsic gene expression subset data, baseline molecular pathway information, and serum biomarkers along with surrogate measures of modified Rodnan skin score provides molecular context in SSc clinical trials. With validation, these approaches could be used to match patients with the therapies from which they are most likely to benefit and thus increase the likelihood of clinical improvement.

  8. A Case Study on E - Banking Security – When Security Becomes Too Sophisticated for the User to Access Their Information

    OpenAIRE

    Aaron M. French

    2012-01-01

    While eBanking security continues to increase in sophistication to protect against threats, the usability of the eBanking decreases resulting in poor security behaviors by the users. The current research evaluates se curity risks and measures taken for eBanking solutions. A case study is presented describing how increased complexity decreases vulnerabilities online but increases vulnerabilities from internal threats and eBanking users

  9. The effects of ecstasy on neurotransmitter systems: a review on the findings of molecular imaging studies.

    Science.gov (United States)

    Vegting, Yosta; Reneman, Liesbeth; Booij, Jan

    2016-10-01

    Ecstasy is a commonly used psychoactive drug with 3,4-methylenedioxymethamphetamine (MDMA) as the main content. Importantly, it has been suggested that use of MDMA may be neurotoxic particularly for serotonergic (5-hydroxytryptamine (5-HT)) neurons. In the past decades, several molecular imaging studies examined directly in vivo the effects of ecstasy/MDMA on neurotransmitter systems. The objective of the present study is to review the effects of ecstasy/MDMA on neurotransmitter systems as assessed by molecular imaging studies in small animals, non-human primates and humans. A search in PubMed was performed. Eighty-eight articles were found on which inclusion and exclusion criteria were applied. Thirty-three studies met the inclusion criteria; all were focused on the 5-HT or dopamine (DA) system. Importantly, 9 out of 11 of the animal studies that examined the effects of MDMA on 5-HT transporter (SERT) availability showed a significant loss of binding potential. In human studies, this was the case for 14 out of 16 studies, particularly in heavy users. In abstinent users, significant recovery of SERT binding was found over time. Most imaging studies in humans that focused on the DA system did not find any significant effect of ecstasy/MDMA use. Preclinical and clinical molecular imaging studies on the effects of ecstasy/MDMA use/administration on neurotransmitter systems show quite consistent alterations of the 5-HT system. Particularly, in human studies, loss of SERT binding was observed in heavy ecstasy users, which might reflect 5-HT neurotoxicity, although alternative explanations (e.g. down-regulation of the SERT) cannot be excluded.

  10. Reclamation of a molecular beam epitaxy system and conversion for oxide epitaxy

    International Nuclear Information System (INIS)

    Carver, Alexander G.; Henderson, Walter; Doolittle, W. Alan

    2008-01-01

    An early 1980s vintage molecular beam epitaxy system, a Varian Gen II system, originally used for HgCdTe epitaxy, was converted into a system capable of growing thin-film complex metal oxides. The nature of some of the alternative oxides requires a thorough cleaning and, in some cases, complete replacement of system components. Details are provided regarding the chemistry of the etchants used, safety requirements for properly handling, and disposal of large quantities of etchants and etch by-products, and components that can be reused versus components that require replacement are given. Following the given procedures, an ultimate base pressure of 2x10 -10 Torr was obtained. Films grown in the system after reclamation contained no evidence of previously present materials down to the detection limit of secondary ion mass spectrometry

  11. Mathematical models of non-linear phenomena, processes and systems: from molecular scale to planetary atmosphere

    CERN Document Server

    2013-01-01

    This book consists of twenty seven chapters, which can be divided into three large categories: articles with the focus on the mathematical treatment of non-linear problems, including the methodologies, algorithms and properties of analytical and numerical solutions to particular non-linear problems; theoretical and computational studies dedicated to the physics and chemistry of non-linear micro-and nano-scale systems, including molecular clusters, nano-particles and nano-composites; and, papers focused on non-linear processes in medico-biological systems, including mathematical models of ferments, amino acids, blood fluids and polynucleic chains.

  12. Unraveling the effect of the hydration level on the molecular mobility of nanolayered polymeric systems.

    Science.gov (United States)

    Borges, João; Caridade, Sofia G; Silva, Joana M; Mano, João F

    2015-02-01

    This work investigates the influence of the hydration level on the molecular mobility and glass transition dynamics of freestanding chitosan/alginate (CHT/ALG) nanolayered systems. Nonconventional dynamic mechanical analysis identifies two relaxation processes assigned to the α-relaxation of the two biopolymers, respectively, CHT and ALG, when immersed in water/ethanol mixtures. This phenomenon explains the shape memory properties of the multilayered systems induced by hydration, thus constituting promising smart materials that would be of paramount importance in a plethora of research fields, including in the biomedical and biotechnological fields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Optical activity of oriented molecular systems in terms of the magnetoelectric tensor of gyrotropy

    International Nuclear Information System (INIS)

    Arteaga, Oriol

    2014-01-01

    The optical activity of oriented molecular systems is investigated using bianisotropic material constitutives for Maxwell's equations. It is shown that the circular birefringence and circular dichroism for an oriented system can be conveniently expressed in terms of the two components of the symmetric magnetoelectric tensor of gyrotropy that are perpendicular to this direction of light propagation. This description establishes a direct link between the optical activity measured at a certain direction and the tensors that describe the oscillating electric and magnetic dipole and electric quadrupole moments induced by the optical wave. (paper)

  14. Preliminary Design of Molecular Sieve for Removing Organic Iodide in Containment Filtered Venting System

    Energy Technology Data Exchange (ETDEWEB)

    Park, Tong Kyu; Shin, So Eun; Lee, Byung Chul [Heungdeok IT Valley Bldg., Yongin (Korea, Republic of); Kim, Hong Hyun; Lee, Kyung Jun [Gemvax and KAEL Inc., Daejeon (Korea, Republic of)

    2014-05-15

    In this paper, to increase the DF for gaseous iodine species, especially organic iodide, molecular sieve filled by silver exchanged zeolites is proposed and designed preliminarily. Its aerodynamic analysis is also performed and presented. In order to increase the DF for gaseous organic iodide, deep-bed type molecular sieve was proposed and designed preliminarily. Total 1,620kg of silver exchanged zeolites were filled evenly in 10 beds of the molecular sieve. The safety factor in the case of 20m{sup 3}/s will be smaller than the counterpart of the standard case (6m{sup 3}/s). However, if the adsorption capacity of the zeolites is larger than 3.09mg/g when the residence time is 0.09 second, the designed molecular sieve can be used at 20m3/s of volumetric flow rate. The removal efficiency for organic iodide should be considered as well as economical aspects in the design of molecular sieve. In the event of nuclear power plant (NPP) severe accident, the nuclear reactor containment might suffer damage resulting from overpressure caused by decay heat. In order to prevent this containment damage, containment venting has been considered as one of effective methods. However, since vented gases contain radioactive fission products, they should be filtered to be released to environment. Generally, containment filtered venting system (CFVS) is installed on NPP to achieve this aim. Even though great amount of efforts have been devoted to developing the CFVS using various filtering methods, the decontaminant factor (DF) for radioactive gaseous iodide is still unsatisfactory while DFs for radioactive aerosols and elemental iodine are very high.

  15. Molecular depth profiling of multi-layer systems with cluster ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Juan [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Winograd, Nicholas [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)]. E-mail: nxw@psu.edu

    2006-07-30

    Cluster bombardment of molecular films has created new opportunities for SIMS research. To more quantitatively examine the interaction of cluster beams with organic materials, we have developed a reproducible platform consisting of a well-defined sugar film (trehalose) doped with peptides. Molecular depth profiles have been acquired with these systems using C{sub 60} {sup +} bombardment. In this study, we utilize this platform to determine the feasibility of examining buried interfaces for multi-layer systems. Using C{sub 60} {sup +} at 20 keV, several systems have been tested including Al/trehalose/Si, Al/trehalose/Al/Si, Ag/trehalose/Si and ice/trehalose/Si. The results show that there can be interactions between the layers during the bombardment process that prevent a simple interpretation of the depth profile. We find so far that the best results are obtained when the mass of the overlayer atoms is less than or nearly equal to the mass of the atoms in buried molecules. In general, these observations suggest that C{sub 60} {sup +} bombardment can be successfully applied to interface characterization of multi-layer systems if the systems are carefully chosen.

  16. Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.

    Science.gov (United States)

    Hudson, Marie; Bernatsky, Sasha; Colmegna, Ines; Lora, Maximilien; Pastinen, Tomi; Klein Oros, Kathleen; Greenwood, Celia M T

    2017-06-03

    We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4 + T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases. We recruited 13 seropositive rheumatoid arthritis, 19 systemic sclerosis, 12 systemic lupus erythematosus subjects, and 8 healthy controls. We identified 33 genes that were both differentially methylated and expressed (26 over- and 7 under-expressed) in SARD cases versus controls. The most highly overexpressed gene was CD1C (log fold change in expression = 1.85, adjusted P value = 0.009). In functional analysis (Ingenuity Pathway Analysis), the top network identified was lipid metabolism, molecular transport, small molecule biochemistry. The top canonical pathways included the mitochondrial L-carnitine shuttle pathway (P = 5E-03) and PTEN signaling (P = 8E-03). The top upstream regulator was HNF4A (P = 3E-05). This novel SARD signature contributes to ongoing work to further our understanding of the molecular mechanisms underlying SARD and provides novel targets of interest.

  17. System geometry optimization for molecular breast tomosynthesis with focusing multi-pinhole collimators

    Science.gov (United States)

    van Roosmalen, Jarno; Beekman, Freek J.; Goorden, Marlies C.

    2018-01-01

    Imaging of 99mTc-labelled tracers is gaining popularity for detecting breast tumours. Recently, we proposed a novel design for molecular breast tomosynthesis (MBT) based on two sliding focusing multi-pinhole collimators that scan a modestly compressed breast. Simulation studies indicate that MBT has the potential to improve the tumour-to-background contrast-to-noise ratio significantly over state-of-the-art planar molecular breast imaging. The aim of the present paper is to optimize the collimator-detector geometry of MBT. Using analytical models, we first optimized sensitivity at different fixed system resolutions (ranging from 5 to 12 mm) by tuning the pinhole diameters and the distance between breast and detector for a whole series of automatically generated multi-pinhole designs. We evaluated both MBT with a conventional continuous crystal detector with 3.2 mm intrinsic resolution and with a pixelated detector with 1.6 mm pixels. Subsequently, full system simulations of a breast phantom containing several lesions were performed for the optimized geometry at each system resolution for both types of detector. From these simulations, we found that tumour-to-background contrast-to-noise ratio was highest for systems in the 7 mm-10 mm system resolution range over which it hardly varied. No significant differences between the two detector types were found.

  18. Positron annihilation lifetime spectroscopy (PALS): a probe for molecular organisation in self-assembled biomimetic systems.

    Science.gov (United States)

    Fong, Celesta; Dong, Aurelia W; Hill, Anita J; Boyd, Ben J; Drummond, Calum J

    2015-07-21

    Positron annihilation lifetime spectroscopy (PALS) has been shown to be highly sensitive to conformational, structural and microenvironmental transformations arising from subtle geometric changes in molecular geometry in self-assembling biomimetic systems. The ortho-positronium (oPs) may be considered an active probe that can provide information on intrinsic packing and mobility within low molecular weight solids, viscous liquids, and soft matter systems. In this perspective we provide a critical overview of the literature in this field, including the evolution of analysis software and experimental protocols with commentary upon the practical utility of PALS. In particular, we discuss how PALS can provide unique insight into the macroscopic transport properties of several porous biomembrane-like nanostructures and suggest how this insight may provide information on the release of drugs from these matrices to aid in developing therapeutic interventions. We discuss the potentially exciting and fruitful application of this technique to membrane dynamics, diffusion and permeability. We propose that PALS can provide novel molecular level information that is complementary to conventional characterisation techniques.

  19. A neural network approach to the study of internal energy flow in molecular systems

    International Nuclear Information System (INIS)

    Sumpter, B.G.; Getino, C.; Noid, D.W.

    1992-01-01

    Neural networks are used to develop a new technique for efficient analysis of data obtained from molecular-dynamics calculations and is applied to the study of mode energy flow in molecular systems. The methodology is based on teaching an appropriate neural network the relationship between phase-space points along a classical trajectory and mode energies for stretch, bend, and torsion vibrations. Results are discussed for reactive and nonreactive classical trajectories of hydrogen peroxide (H 2 O 2 ) on a semiempirical potential-energy surface. The neural-network approach is shown to produce reasonably accurate values for the mode energies, with average errors between 1% and 12%, and is applicable to any region within the 24-dimensional phase space of H 2 O 2 . In addition, the generic knowledge learned by the neural network allows calculations to be made for other molecular systems. Results are discussed for a series of tetratomic molecules: H 2 X 2 , X=C, N, O, Si, S, or Se, and preliminary results are given for energy flow predictions in macromolecules

  20. Theoretical study on the molecular tautomerism of the 3-hydroxy-pyridin-4-one system

    Science.gov (United States)

    Zborowski, Krzysztof K.; Mohammadpour, Mehrdad; Sadeghi, Amir; Proniewicz, Leonard M.

    2013-04-01

    3-hydroxy-pyridin-4-one is a parent molecule for the family of hydroxypyridinones that are known in coordination chemistry as efficient metal ions chelators. In this work, relative stabilities of some possible tautomers were investigated using several quantum chemical methods: CBS (complete basis set methods), Gn, DFT (density functional theory), Hartree-Fock and MP2. Performed calculations show that the system under consideration exists as a mixture of two tautomers with comparable energies. Among them, the hydroxypyridinone structure of the studied molecular system seems to be a bit more stable than the o-dihydroxypyridine one, by a few kJ/mol only. Aromaticity and intra-molecular hydrogen bonding are the main effects influencing the stability of the studied tautomeric structures. Consequently, aromatic effects were calculated using several indices of aromaticity: HOMA (harmonic oscillator model of aromaticity), NICS (nucleus independent chemical shift), H, PDI (para delocalisation index), MCI (multi-centre index) and ASE (aromatic stabilisation energy). The strength of possible intra-molecular hydrogen bonds (H-bonds) was determined by means of the AIM (atoms-in-molecules) method and by calculating enthalpies for theoretical reactions that do or do not involve H-bonds. The AIM method was employed to understand how variations in atomic energies influence the stability of different tautomeric structures.

  1. A Protoplast Transient Expression System to Enable Molecular, Cellular, and Functional Studies in Phalaenopsis orchids

    Directory of Open Access Journals (Sweden)

    Hsiang-Yin Lin

    2018-06-01

    Full Text Available The enigmatic nature of the specialized developmental programs of orchids has fascinated plant biologists for centuries. The recent releases of orchid genomes indicate that orchids possess new gene families and family expansions and contractions to regulate a diverse suite of developmental processes. However, the extremely long orchid life cycle and lack of molecular toolkit have hampered the advancement of orchid biology research. To overcome the technical difficulties and establish a platform for rapid gene regulation studies, in this study, we developed an efficient protoplast isolation and transient expression system for Phalaenopsis aphrodite. This protocol was successfully applied to protein subcellular localization and protein–protein interaction studies. Moreover, it was confirmed to be useful in delineating the PaE2F/PaDP-dependent cell cycle pathway and studying auxin response. In summary, the established orchid protoplast transient expression system provides a means to functionally characterize orchid genes at the molecular level allowing assessment of transcriptome responses to transgene expression and widening the scope of molecular studies in orchids.

  2. MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.

    Science.gov (United States)

    Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto

    2014-08-06

    We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(-1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.

  3. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    Science.gov (United States)

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

  4. Self-consistent field theory based molecular dynamics with linear system-size scaling

    Energy Technology Data Exchange (ETDEWEB)

    Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

    2014-04-07

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  5. A molecular dynamics simulation of sodium pentadecyl sulphonate (SPDS)/water system

    International Nuclear Information System (INIS)

    Arsenyan, L.H.; Poghosyan, A.H.; Shahinyan, A.A.

    2008-07-01

    We have carried out a molecular dynamics simulation of a sodium pentadecylsulfonate (SPDS)/water system consisting of 64PDS/1200water and 512PDS/9000water molecules, correspondingly. The overall simulation time for both cases reaches up to 60ns and the simulation was performed using the NAMD code with CHARMM27 force field. The main parameters of the system have been calculated and compared with available X-ray diffraction findings. For large system, after a couple of ns, we receive the molecule's hydrocarbon chains tilt in the opposite sense in layers and reducing the system size leads to the decrease of the average angle between bilayer normal and chain vector. At the end of 50ns of a simulation run we achieve the crystalline-like structure of hydrocarbon packing. For both cases, we obtain tilted hydrocarbon chains packing and the average angle between bilayer normal and chain vector is estimated to be about 13 deg. and 10 deg. (author)

  6. Molecular Mechanisms Underlying Renin-Angiotensin-Aldosterone System Mediated Regulation of BK Channels

    Directory of Open Access Journals (Sweden)

    Zhen-Ye Zhang

    2017-09-01

    Full Text Available Large-conductance calcium-activated potassium channels (BK channels belong to a family of Ca2+-sensitive voltage-dependent potassium channels and play a vital role in various physiological activities in the human body. The renin-angiotensin-aldosterone system is acknowledged as being vital in the body's hormone system and plays a fundamental role in the maintenance of water and electrolyte balance and blood pressure regulation. There is growing evidence that the renin-angiotensin-aldosterone system has profound influences on the expression and bioactivity of BK channels. In this review, we focus on the molecular mechanisms underlying the regulation of BK channels mediated by the renin-angiotensin-aldosterone system and its potential as a target for clinical drugs.

  7. DEVELOPMENT OF SEPARATION SYSTEMS FOR POLYNUCLEAR AROMATIC HYDROCARBON ENVIRONMENTAL CONTAMINANTS USING MICELLAR ELECTROKINETIC CHROMATOGRAPHY WITH MOLECULAR MICELLES AND FREE ZONE ELECTROPHORESIS

    Science.gov (United States)

    Of four systems available from the literature, based on cyclodextrins, dioctylsulfosuccinate, bile salts, and molecular micelles consisting of oligomers of undecylenic acid, the most successful separation system in our hands is based on the molecular micelles, oligomers of sodiu...

  8. A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

    Science.gov (United States)

    Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

    2016-07-01

    A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ

  9. A sophisticated cad tool for the creation of complex models for electromagnetic interaction analysis

    Science.gov (United States)

    Dion, Marc; Kashyap, Satish; Louie, Aloisius

    1991-06-01

    This report describes the essential features of the MS-DOS version of DIDEC-DREO, an interactive program for creating wire grid, surface patch, and cell models of complex structures for electromagnetic interaction analysis. It uses the device-independent graphics library DIGRAF and the graphics kernel system HALO, and can be executed on systems with various graphics devices. Complicated structures can be created by direct alphanumeric keyboard entry, digitization of blueprints, conversion form existing geometric structure files, and merging of simple geometric shapes. A completed DIDEC geometric file may then be converted to the format required for input to a variety of time domain and frequency domain electromagnetic interaction codes. This report gives a detailed description of the program DIDEC-DREO, its installation, and its theoretical background. Each available interactive command is described. The associated program HEDRON which generates simple geometric shapes, and other programs that extract the current amplitude data from electromagnetic interaction code outputs, are also discussed.

  10. Information theory and signal transduction systems: from molecular information processing to network inference.

    Science.gov (United States)

    Mc Mahon, Siobhan S; Sim, Aaron; Filippi, Sarah; Johnson, Robert; Liepe, Juliane; Smith, Dominic; Stumpf, Michael P H

    2014-11-01

    Sensing and responding to the environment are two essential functions that all biological organisms need to master for survival and successful reproduction. Developmental processes are marshalled by a diverse set of signalling and control systems, ranging from systems with simple chemical inputs and outputs to complex molecular and cellular networks with non-linear dynamics. Information theory provides a powerful and convenient framework in which such systems can be studied; but it also provides the means to reconstruct the structure and dynamics of molecular interaction networks underlying physiological and developmental processes. Here we supply a brief description of its basic concepts and introduce some useful tools for systems and developmental biologists. Along with a brief but thorough theoretical primer, we demonstrate the wide applicability and biological application-specific nuances by way of different illustrative vignettes. In particular, we focus on the characterisation of biological information processing efficiency, examining cell-fate decision making processes, gene regulatory network reconstruction, and efficient signal transduction experimental design. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

    Science.gov (United States)

    Bolhuis, Peter

    Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

  12. Sophisticated lessons from simple organisms: appreciating the value of curiosity-driven research

    Directory of Open Access Journals (Sweden)

    Robert J. Duronio

    2017-12-01

    Full Text Available For hundreds of years, biologists have studied accessible organisms such as garden peas, sea urchins collected at low tide, newt eggs, and flies circling rotten fruit. These organisms help us to understand the world around us, attracting and inspiring each new generation of biologists with the promise of mystery and discovery. Time and time again, what we learn from such simple organisms has emphasized our common biological origins by proving to be applicable to more complex organisms, including humans. Yet, biologists are increasingly being tasked with developing applications from the known, rather than being allowed to follow a path to discovery of the as yet unknown. Here, we provide examples of important lessons learned from research using selected non-vertebrate organisms. We argue that, for the purpose of understanding human disease, simple organisms cannot and should not be replaced solely by human cell-based culture systems. Rather, these organisms serve as powerful discovery tools for new knowledge that could subsequently be tested for conservation in human cell-based culture systems. In this way, curiosity-driven biological research in simple organisms has and will continue to pay huge dividends in both the short and long run for improving the human condition.

  13. Proteomic approach toward molecular backgrounds of drug resistance of osteosarcoma cells in spheroid culture system.

    Science.gov (United States)

    Arai, Kazuya; Sakamoto, Ruriko; Kubota, Daisuke; Kondo, Tadashi

    2013-08-01

    Chemoresistance is one of the most critical prognostic factors in osteosarcoma, and elucidation of the molecular backgrounds of chemoresistance may lead to better clinical outcomes. Spheroid cells resemble in vivo cells and are considered an in vitro model for the drug discovery. We found that spheroid cells displayed more chemoresistance than conventional monolayer cells across 11 osteosarcoma cell lines. To investigate the molecular mechanisms underlying the resistance to chemotherapy, we examined the proteomic differences between the monolayer and spheroid cells by 2D-DIGE. Of the 4762 protein species observed, we further investigated 435 species with annotated mass spectra in the public proteome database, Genome Medicine Database of Japan Proteomics. Among the 435 protein species, we found that 17 species exhibited expression level differences when the cells formed spheroids in more than five cell lines and four species out of these 17 were associated with spheroid-formation associated resistance to doxorubicin. We confirmed the upregulation of cathepsin D in spheroid cells by western blotting. Cathepsin D has been implicated in chemoresistance of various malignancies but has not previously been implemented in osteosarcoma. Our study suggested that the spheroid system may be a useful tool to reveal the molecular backgrounds of chemoresistance in osteosarcoma. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Molecular transformation, gene cloning, and gene expression systems for filamentous fungi

    Science.gov (United States)

    Gold, Scott E.; Duick, John W.; Redman, Regina S.; Rodriguez, Rusty J.

    2001-01-01

    This chapter discusses the molecular transformation, gene cloning, and gene expression systems for filamentous fungi. Molecular transformation involves the movement of discrete amounts of DNA into cells, the expression of genes on the transported DNA, and the sustainable replication of the transforming DNA. The ability to transform fungi is dependent on the stable replication and expression of genes located on the transforming DNA. Three phenomena observed in bacteria, that is, competence, plasmids, and restriction enzymes to facilitate cloning, were responsible for the development of molecular transformation in fungi. Initial transformation success with filamentous fungi, involving the complementation of auxotrophic mutants by exposure to sheared genomic DNA or RNA from wt isolates, occurred with low transformation efficiencies. In addition, it was difficult to retrieve complementing DNA fragments and isolate genes of interest. This prompted the development of transformation vectors and methods to increase efficiencies. The physiological studies performed with fungi indicated that the cell wall could be removed to generate protoplasts. It was evident that protoplasts could be transformed with significantly greater efficiencies than walled cells.

  15. Solar fuels generation and molecular systems: is it homogeneous or heterogeneous catalysis?

    Science.gov (United States)

    Artero, Vincent; Fontecave, Marc

    2013-03-21

    Catalysis is a key enabling technology for solar fuel generation. A number of catalytic systems, either molecular/homogeneous or solid/heterogeneous, have been developed during the last few decades for both the reductive and oxidative multi-electron reactions required for fuel production from water or CO(2) as renewable raw materials. While allowing for a fine tuning of the catalytic properties through ligand design, molecular approaches are frequently criticized because of the inherent fragility of the resulting catalysts, when exposed to extreme redox potentials. In a number of cases, it has been clearly established that the true catalytic species is heterogeneous in nature, arising from the transformation of the initial molecular species, which should rather be considered as a pre-catalyst. Whether such a situation is general or not is a matter of debate in the community. In this review, covering water oxidation and reduction catalysts, involving noble and non-noble metal ions, we limit our discussion to the cases in which this issue has been directly and properly addressed as well as those requiring more confirmation. The methodologies proposed for discriminating homogeneous and heterogeneous catalysis are inspired in part by those previously discussed by Finke in the case of homogeneous hydrogenation reaction in organometallic chemistry [J. A. Widegren and R. G. Finke, J. Mol. Catal. A, 2003, 198, 317-341].

  16. Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

    Energy Technology Data Exchange (ETDEWEB)

    Tsourtis, Anastasios, E-mail: tsourtis@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, Crete (Greece); Pantazis, Yannis, E-mail: pantazis@math.umass.edu; Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-70013 Heraklion, Crete (Greece)

    2015-07-07

    In this paper, we present a parametric sensitivity analysis (SA) methodology for continuous time and continuous space Markov processes represented by stochastic differential equations. Particularly, we focus on stochastic molecular dynamics as described by the Langevin equation. The utilized SA method is based on the computation of the information-theoretic (and thermodynamic) quantity of relative entropy rate (RER) and the associated Fisher information matrix (FIM) between path distributions, and it is an extension of the work proposed by Y. Pantazis and M. A. Katsoulakis [J. Chem. Phys. 138, 054115 (2013)]. A major advantage of the pathwise SA method is that both RER and pathwise FIM depend only on averages of the force field; therefore, they are tractable and computable as ergodic averages from a single run of the molecular dynamics simulation both in equilibrium and in non-equilibrium steady state regimes. We validate the performance of the extended SA method to two different molecular stochastic systems, a standard Lennard-Jones fluid and an all-atom methane liquid, and compare the obtained parameter sensitivities with parameter sensitivities on three popular and well-studied observable functions, namely, the radial distribution function, the mean squared displacement, and the pressure. Results show that the RER-based sensitivities are highly correlated with the observable-based sensitivities.

  17. Improved Fab presentation on phage surface with the use of molecular chaperone coplasmid system.

    Science.gov (United States)

    Loh, Qiuting; Leong, Siew Wen; Tye, Gee Jun; Choong, Yee Siew; Lim, Theam Soon

    2015-05-15

    The low presentation efficiency of Fab (fragment antigen binding) fragments during phage display is largely due to the complexity of disulphide bond formation. This can result in the presentation of Fab fragments devoid of a light chain during phage display. Here we propose the use of a coplasmid system encoding several molecular chaperones (DsbA, DsbC, FkpA, and SurA) to improve Fab packaging. A comparison was done using the Fab fragment from IgG and IgD. We found that the use of the coplasmid during phage packaging was able to improve the presentation efficiency of the Fab fragment on phage surfaces. A modified version of panning using the coplasmid system was evaluated and was successful at enriching Fab binders. Therefore, the coplasmid system would be an attractive alternative for improved Fab presentation for phage display. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Molecular players involved in the interaction between beneficial bacteria and the immune system

    Directory of Open Access Journals (Sweden)

    Arancha eHevia

    2015-11-01

    Full Text Available The human gastrointestinal tract is a very complex ecosystem, in which there is a continuous interaction between nutrients, host cells, and microorganisms. The gut microbiota comprises trillions of microbes that have been selected during evolution on the basis of their functionality and capacity to survive in, and adapt to, the intestinal environment. Host bacteria and our immune system constantly sense and react to one another. In this regard, commensal microbes contribute to gut homeostasis, whereas the necessary responses are triggered against enteropathogens. Some representatives of our gut microbiota have beneficial effects on human health. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins, or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function. This process is mainly performed via the pattern recognition receptors of epithelial cells, such as Toll-like or Nod-like receptors, which are able to recognize the molecular effectors that are produced by intestinal microbes. These effectors mediate processes that can ameliorate certain inflammatory gut disorders, discriminate between beneficial and pathogenic bacteria, or increase the number of immune cells or their pattern recognition receptors. This review intends to summarize the molecular players produced by probiotic bacteria, notably Lactobacillus and Bifidobacterium strains, but also other very promising potential probiotics, which affect the human immune system.

  19. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    Science.gov (United States)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

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

    Science.gov (United States)

    Citroni, Margherita

    2013-06-01

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

  1. Membrane Lipid Oscillation: An Emerging System of Molecular Dynamics in the Plant Membrane.

    Science.gov (United States)

    Nakamura, Yuki

    2018-03-01

    Biological rhythm represents a major biological process of living organisms. However, rhythmic oscillation of membrane lipid content is poorly described in plants. The development of lipidomic technology has led to the illustration of precise molecular profiles of membrane lipids under various growth conditions. Compared with conventional lipid signaling, which produces unpredictable lipid changes in response to ever-changing environmental conditions, lipid oscillation generates a fairly predictable lipid profile, adding a new layer of biological function to the membrane system and possible cross-talk with the other chronobiological processes. This mini review covers recent studies elucidating membrane lipid oscillation in plants.

  2. Molecular Thermodynamic Modeling and Design of Microencapsulation Systems for Drug Delivery

    DEFF Research Database (Denmark)

    Abildskov, Jens; O’Connell, John P.

    2011-01-01

    is based on fundamental thermodynamic relations and group contributions to properties of pure species (solvent, active ingredient and polymer) and their mixtures. The method is intended for pharmaceuticals with complex molecular structures, for which limited experimental information is known. Case studies......A systematic design strategy is given for computer-aided design of microparticle drug-delivery systems produced by solvent evaporation. In particular, design of solvents, polymer material, and external phase composition are considered for the case when the active ingredient is known. The procedure...... of solvent design are given....

  3. Studying the Impact of Spaceflight Environment on Immune Functions Using New Molecular Diagnostics System

    Science.gov (United States)

    Cohen, Luchino

    Immune functions are altered during space flights. Latent virus reactivation, reduction in the number of immune cells, decreased cell activation and increased sensitivity of astronauts to infections following their return on Earth demonstrate that the immune system is less efficient during space flight. The causes of this immune deficiency are not fully understood and this dysfunction during long-term missions could result in the appearance of opportunistic infections or a decrease in the immuno-surveillance mechanisms that eradicate cancer cells. Therefore, the immune functions of astronauts will have to be monitored continuously during long-term missions in space, using miniature and semi-automated diagnostic systems. The objectives of this project are to study the causes of space-related immunodeficiency, to develop countermeasures to maintain an optimal immune function and to improve our capacity to detect infectious diseases during space missions through the monitoring of astronauts' immune system. In order to achieve these objectives, an Immune Function Diagnostic System (IFDS) will be designed to perform a set of immunological assays on board spacecrafts or on planet-bound bases. Through flow cytometric assays and molecular biology analyses, this diagnostic system could improve medical surveillance of astronauts and could be used to test countermeasures aimed at preventing immune deficiency during space missions. The capacity of the instrument to assess cellular fluorescence and to quantify the presence of soluble molecules in biological samples would support advanced molecular studies in space life sciences. Finally, such diagnostic system could also be used on Earth in remote areas or in mobile hospitals following natural disasters to fight against infectious diseases and other pathologies.

  4. Flexible and Versatile as a Chameleon—Sophisticated Functions of microRNA-199a

    Directory of Open Access Journals (Sweden)

    Shen Gu

    2012-07-01

    Full Text Available Although widely studied in the past decade, our knowledge of the functional role of microRNAs (miRNAs remains limited. Among the many miRNAs identified in humans, we focus on miR-199a due to its varied and important functions in diverse models and systems. Its expression is finely regulated by promoter methylation and direct binding of transcription factors such as TWIST1. During tumorigenesis, depending on the nature of the cancer, miR-199a, especially its -3p mature form, may act as either a potential tumor suppressor or an oncogene. Its 5p mature form has been shown to protect cardiomyocytes from hypoxic damage via its action on HIF1α. It also has a functional role in stem cell differentiation, embryo development, hepatitis, liver fibrosis, etc. Though it has varied biological activities, its regulation has not been reviewed. The varied and protean functions of miR-199a suggest that efforts to generalize the action of a miRNA are problematic. This review provides a comprehensive survey of the literature on miR-199a as an example of the complexity of miRNA biology and suggests future directions for miRNA research.

  5. Experimental study on seismic behaviors of two-storied sophisticated model for nuclear reactor building

    Energy Technology Data Exchange (ETDEWEB)

    Higashiura, Akira; Sato, Kazuhide; Muramoto, Michiya; Yanagase, Takahito; Watanabe, Satoshi

    1987-03-01

    In this paper, by pseudo dynamic test using substructuring technique and lateral static loading test, authors wish to introduce the investigation on the seismic behaviors of nuclear reactor building. The results obtained by those test are as follows. 1) The maximum response displacements obtained by pseudo dynamic test are equivalent to those by dynamic analytical procedures using the approximate earthquake ground motion. 2) In the finally stage of pseudo dynamic test, the natural period of the system is increased about three times as long as that in elastic region. 3) Some shear cracks is observed on the web portion of the box and the truncated conical wall at the end of pseudo dynamic test. 4) Maximum shear forces in the test specimen obtained by pseudo dynamic test are about one third of the ultimate shear strength of it obtained by static loading test. 5) At the ultimate strength of the test specimen on static loading test, a lot of shear cracks and crush of concrete are observed on web portion of the box and the truncated conical wall.

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

    Science.gov (United States)

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

    2011-09-01

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

  7. Workable male sterility systems for hybrid rice: Genetics, biochemistry, molecular biology, and utilization.

    Science.gov (United States)

    Huang, Jian-Zhong; E, Zhi-Guo; Zhang, Hua-Li; Shu, Qing-Yao

    2014-12-01

    The exploitation of male sterility systems has enabled the commercialization of heterosis in rice, with greatly increased yield and total production of this major staple food crop. Hybrid rice, which was adopted in the 1970s, now covers nearly 13.6 million hectares each year in China alone. Various types of cytoplasmic male sterility (CMS) and environment-conditioned genic male sterility (EGMS) systems have been applied in hybrid rice production. In this paper, recent advances in genetics, biochemistry, and molecular biology are reviewed with an emphasis on major male sterility systems in rice: five CMS systems, i.e., BT-, HL-, WA-, LD- and CW- CMS, and two EGMS systems, i.e., photoperiod- and temperature-sensitive genic male sterility (P/TGMS). The interaction of chimeric mitochondrial genes with nuclear genes causes CMS, which may be restored by restorer of fertility (Rf) genes. The PGMS, on the other hand, is conditioned by a non-coding RNA gene. A survey of the various CMS and EGMS lines used in hybrid rice production over the past three decades shows that the two-line system utilizing EGMS lines is playing a steadily larger role and TGMS lines predominate the current two-line system for hybrid rice production. The findings and experience gained during development and application of, and research on male sterility in rice not only advanced our understanding but also shed light on applications to other crops.

  8. Fragment-orbital tunneling currents and electronic couplings for analysis of molecular charge-transfer systems.

    Science.gov (United States)

    Hwang, Sang-Yeon; Kim, Jaewook; Kim, Woo Youn

    2018-04-04

    In theoretical charge-transfer research, calculation of the electronic coupling element is crucial for examining the degree of the electronic donor-acceptor interaction. The tunneling current (TC), representing the magnitudes and directions of electron flow, provides a way of evaluating electronic couplings, along with the ability of visualizing how electrons flow in systems. Here, we applied the TC theory to π-conjugated organic dimer systems, in the form of our fragment-orbital tunneling current (FOTC) method, which uses the frontier molecular-orbitals of system fragments as diabatic states. For a comprehensive test of FOTC, we assessed how reasonable the computed electronic couplings and the corresponding TC densities are for the hole- and electron-transfer databases HAB11 and HAB7. FOTC gave 12.5% mean relative unsigned error with regard to the high-level ab initio reference. The shown performance is comparable with that of fragment-orbital density functional theory, which gave the same error by 20.6% or 13.9% depending on the formulation. In the test of a set of nucleobase π stacks, we showed that the original TC expression is also applicable to nondegenerate cases under the condition that the overlap between the charge distributions of diabatic states is small enough to offset the energy difference. Lastly, we carried out visual analysis on the FOTC densities of thiophene dimers with different intermolecular alignments. The result depicts an intimate topological connection between the system geometry and electron flow. Our work provides quantitative and qualitative grounds for FOTC, showing it to be a versatile tool in characterization of molecular charge-transfer systems.

  9. Radiopharmaceuticals: nanoparticles like multi-functional systems for the obtaining in vivo of molecular images; Radiofarmacos: nanoparticulas como sistemas multifuncionales para la obtencion in vivo de imagenes moleculares

    Energy Technology Data Exchange (ETDEWEB)

    Ferro F, G.; Ramirez de la Cruz, F. M.; Ocampo G, B. E.; Morales A, E.; Santos C, C. L.; Mendoza S, A. N., E-mail: guillermina.ferro@inin.gob.m [ININ, Departamento de Materiales Radiactivos, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

    2010-07-01

    The techniques of obtaining direct or indirect molecular images detect and register the space-temporary distribution of molecular or cellular processes for biochemical, biological, diagnostic and therapeutic applications. The advanced techniques of image like the nuclear magnetic resonance, the single photon emission computed tomography, the positron emission tomography and the images of optic fluorescence have been used successfully to detect these processes. On the other hand, the utility of the nanoparticles for any application is dependent of the physicochemical properties that present, being possible to modify their surface when making them react with different biomolecules what allows the formation of conjugates with specific molecular recognition. The joint of various protein molecules, peptides or oligonucleotides to the surface of a nanoparticle produce a multi-functional system able to increase the multivalent joints from the nanoparticles-biomolecules to their receivers for the obtaining of molecular images in vivo. The peptides stimulate, regulate or inhibit numerous functions of the life, acting mainly as information transmitters and activity coordinators of several tissues in the organism. The receivers of regulator peptides are over represented in numerous types of cancer cells and they are protein structures. These receivers have been used as white molecular of marked peptides, to locate primary malignant tumors and their metastasis, using the diagnostic techniques of molecular image mentioned above, which consist basically on the radio peptides use and conjugated peptides to fluoro chromes, to metallic nanoparticles and nano crystals. A summary of the work is presented carried out by the personnel of the Radio-active Materials and Chemistry Departments of the Instituto Nacional de Investigaciones Nucleares in this field. (Author)

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

    Science.gov (United States)

    Harutyunyan, R. S.

    2013-08-01

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

  11. Molecular Epidemiologic Typing Systems of Bacterial Pathogens: Current Issues and Perpectives

    Directory of Open Access Journals (Sweden)

    Struelens Marc J

    1998-01-01

    Full Text Available The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s ? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection. Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

  12. Molecular – genetic variance of RH blood group system within human population of Bosnia and Herzegovina

    Directory of Open Access Journals (Sweden)

    Lejla Lasić

    2013-02-01

    Full Text Available There are two major theories for inheritance of Rh blood group system: Fisher - Race theory and Wiener theory. Aim of this study was identifying frequency of RHDCE alleles in Bosnian - Herzegovinian population and introduction of this method in screening for Rh phenotype in B&H since this type of analysis was not used for blood typing in B&H before. Rh blood group was typed by Polymerase Chain Reaction, using the protocols and primers previously established by other authors, then carrying out electrophoresis in 2-3% agarose gel. Percentage of Rh positive individuals in our sample is 84.48%, while the percentage of Rh negative individuals is 15.52%. Inter-rater agreement statistic showed perfect agreement (K=1 between the results of Rh blood system detection based on serological and molecular-genetics methods. In conclusion, molecular - genetic methods are suitable for prenatal genotyping and specific cases while standard serological method is suitable for high-throughput of samples.

  13. Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

    Science.gov (United States)

    van Heeswijk, Wally C.; Westerhoff, Hans V.

    2013-01-01

    SUMMARY We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now. PMID:24296575

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

    Science.gov (United States)

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

    2015-01-28

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

  15. Cocaine and MDMA Induce Cellular and Molecular Changes in Adult Neurogenic Systems: Functional Implications

    Directory of Open Access Journals (Sweden)

    Vivian Capilla-Gonzalez

    2011-06-01

    Full Text Available The capacity of the brain to generate new adult neurons is a recent discovery that challenges the old theory of an immutable adult brain. A new and fascinating field of research now focuses on this regenerative process. The two brain systems that constantly produce new adult neurons, known as the adult neurogenic systems, are the dentate gyrus (DG of the hippocampus and the lateral ventricules/olfactory bulb system. Both systems are involved in memory and learning processes. Different drugs of abuse, such as cocaine and MDMA, have been shown to produce cellular and molecular changes that affect adult neurogenesis. This review summarizes the effects that these drugs have on the adult neurogenic systems. The functional relevance of adult neurogenesis is obscured by the functions of the systems that integrate adult neurons. Therefore, we explore the effects that cocaine and MDMA produce not only on adult neurogenesis, but also on the DG and olfactory bulbs. Finally, we discuss the possible role of new adult neurons in cocaine- and MDMA-induced impairments. We conclude that, although harmful drug effects are produced at multiple physiological and anatomical levels, the specific consequences of reduced hippocampus neurogenesis are unclear and require further exploration.

  16. Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics

    Science.gov (United States)

    Jeong, Sinyoung; Kim, Yong-Il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

    2015-03-01

    Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures.

  17. Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems.

    Science.gov (United States)

    Liu, Xinzijian; Liu, Jian

    2018-03-14

    An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties. Its application to several representative one-dimensional and multi-dimensional models demonstrates that MES-PIMD in principle offers a practical tool in either of the diabatic and adiabatic representations for studying exact quantum statistics of complex/large MES systems when the Born-Oppenheimer approximation, Condon approximation, and harmonic bath approximation are broken.

  18. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

    Directory of Open Access Journals (Sweden)

    Peter Spijker

    2010-06-01

    Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

  19. Integrating open-source software applications to build molecular dynamics systems.

    Science.gov (United States)

    Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

    2014-04-05

    Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

  20. Environmental Catastrophes in the Earth's History Due to Solar Systems Encounters with Giant Molecular Clouds

    Science.gov (United States)

    Pavlov, Alexander A.

    2011-01-01

    In its motion through the Milky Way galaxy, the solar system encounters an average density (>=330 H atoms/cubic cm) giant molecular cloud (GMC) approximately every 108 years, a dense (approx 2 x 103 H atoms/cubic cm) GMC every approx 109 years and will inevitably encounter them in the future. However, there have been no studies linking such events with severe (snowball) glaciations in Earth history. Here we show that dramatic climate change can be caused by interstellar dust accumulating in Earth's atmosphere during the solar system's immersion into a dense (approx ,2 x 103 H atoms/cubic cm) GMC. The stratospheric dust layer from such interstellar particles could provide enough radiative forcing to trigger the runaway ice-albedo feedback that results in global snowball glaciations. We also demonstrate that more frequent collisions with less dense GMCs could cause moderate ice ages.

  1. A quantum-mechanics molecular-mechanics scheme for extended systems.

    Science.gov (United States)

    Hunt, Diego; Sanchez, Veronica M; Scherlis, Damián A

    2016-08-24

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

  2. A quantum-mechanics molecular-mechanics scheme for extended systems

    International Nuclear Information System (INIS)

    Hunt, Diego; Scherlis, Damián A; Sanchez, Veronica M

    2016-01-01

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car–Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO 2 anatase (1 0 1) solid–liquid interface. This investigation suggests that the inclusion of a second monolayer of H 2 O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces. (paper)

  3. An e-Commerce like platform enabling bricks-and-mortar stores to use sophisticated product recommender systems

    OpenAIRE

    Keller, Thorben; Raffelsieper, Matthias

    2014-01-01

    Compared to online-retailers, bricks-and-mortar stores have only limited possibilities to understand consumer preferences, their intentions, and their feedback. The first are able to evaluate clickstream data collected on their web-pages alongside the actual purchase data to put together a comprehensive view on individual customers. Bricks-and-mortar stores on the other hand have to rely solely on the evaluation of scanner data collected at the point of sale (POS). Thus, akin to the Event Hor...

  4. A Silicon SPECT System for Molecular Imaging of the Mouse Brain.

    Science.gov (United States)

    Shokouhi, Sepideh; Fritz, Mark A; McDonald, Benjamin S; Durko, Heather L; Furenlid, Lars R; Wilson, Donald W; Peterson, Todd E

    2007-01-01

    We previously demonstrated the feasibility of using silicon double-sided strip detectors (DSSDs) for SPECT imaging of the activity distribution of iodine-125 using a 300-micrometer thick detector. Based on this experience, we now have developed fully customized silicon DSSDs and associated readout electronics with the intent of developing a multi-pinhole SPECT system. Each DSSD has a 60.4 mm × 60.4 mm active area and is 1 mm thick. The strip pitch is 59 micrometers, and the readout of the 1024 strips on each side gives rise to a detector with over one million pixels. Combining four high-resolution DSSDs into a SPECT system offers an unprecedented space-bandwidth product for the imaging of single-photon emitters. The system consists of two camera heads with two silicon detectors stacked one behind the other in each head. The collimator has a focused pinhole system with cylindrical-shaped pinholes that are laser-drilled in a 250 μm tungsten plate. The unique ability to collect projection data at two magnifications simultaneously allows for multiplexed data at high resolution to be combined with lower magnification data with little or no multiplexing. With the current multi-pinhole collimator design, our SPECT system will be capable of offering high spatial resolution, sensitivity and angular sampling for small field-of-view applications, such as molecular imaging of the mouse brain.

  5. Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems.

    Science.gov (United States)

    Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan

    2015-12-03

    Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.

  6. Synthesis and photophysical properties of a novel corrole–anthraquinone–corrole molecular system

    International Nuclear Information System (INIS)

    Sudhakar, Kolanu; Kanaparthi, Ravi Kumar; Kumar, Challa Kiran; Giribabu, Lingamallu

    2014-01-01

    A novel molecular triad (AQ-(H 3 ) 2 ) based on tritolylcorrole and anthraquinone having azomethine-bridge at the pyrrole-β position has been designed and synthesized by following a facile one step reaction. The molecular system, AQ-(H 3 ) 2 is characterized by elemental analysis, MALDI-MS, 1 H-NMR, UV–Visible and fluorescence spectroscopy (steady-state and time-resolved) as well as electrochemical methods. In absorption spectra, prominent changes such as red-shift (∼7 nm) and broadening of the both Soret and Q-bands with respect to their monomer units were observed. The present study supported by density functional theory calculations manifest that there exists a negligible electronic communication in the ground state between the donor tritolylcorrole and acceptor anthraquinone of the triad. However, interestingly, in the triad AQ-(H 3 ) 2 , fluorescence emission of the tritolylcorrole quenched significantly (17–80%) compared to their monomeric units. The emission quenching is attributed to the excited state intramolecular photoinduced electron transfer from donor tritolylcorrole to acceptor anthraquinone and the electron transfer rates (k ET ) are found in the range 4.1×10 8 to 2.4×10 9 s −1 and are found to be solvent dependent. - Highlights: • Molecular triad based on corrole and anthraquinone having azomethine-bridge at pyrrole-β position. • Ground state properties showed that there exist minimum π–π interactions. • Excited state properties showed intramolecular photoinduced electron transfer from corrole to anthraquinone

  7. Synthesis and photophysical properties of a novel corrole–anthraquinone–corrole molecular system

    Energy Technology Data Exchange (ETDEWEB)

    Sudhakar, Kolanu [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India); Kanaparthi, Ravi Kumar [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India); Department of Chemistry, Central University of Kerala, Reverside Transit Campus, Padanakkad, Nileshwar Kasaragod District - 671 314 Kerala (India); Kumar, Challa Kiran [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India); Giribabu, Lingamallu, E-mail: giribabu@iict.res.in [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India)

    2014-09-15

    A novel molecular triad (AQ-(H{sub 3}){sub 2}) based on tritolylcorrole and anthraquinone having azomethine-bridge at the pyrrole-β position has been designed and synthesized by following a facile one step reaction. The molecular system, AQ-(H{sub 3}){sub 2} is characterized by elemental analysis, MALDI-MS, {sup 1}H-NMR, UV–Visible and fluorescence spectroscopy (steady-state and time-resolved) as well as electrochemical methods. In absorption spectra, prominent changes such as red-shift (∼7 nm) and broadening of the both Soret and Q-bands with respect to their monomer units were observed. The present study supported by density functional theory calculations manifest that there exists a negligible electronic communication in the ground state between the donor tritolylcorrole and acceptor anthraquinone of the triad. However, interestingly, in the triad AQ-(H{sub 3}){sub 2}, fluorescence emission of the tritolylcorrole quenched significantly (17–80%) compared to their monomeric units. The emission quenching is attributed to the excited state intramolecular photoinduced electron transfer from donor tritolylcorrole to acceptor anthraquinone and the electron transfer rates (k{sub ET}) are found in the range 4.1×10{sup 8} to 2.4×10{sup 9} s{sup −1} and are found to be solvent dependent. - Highlights: • Molecular triad based on corrole and anthraquinone having azomethine-bridge at pyrrole-β position. • Ground state properties showed that there exist minimum π–π interactions. • Excited state properties showed intramolecular photoinduced electron transfer from corrole to anthraquinone.

  8. Learning Strategic Sophistication

    NARCIS (Netherlands)

    Blume, A.; DeJong, D.V.; Maier, M.

    2005-01-01

    We experimentally investigate coordination games in which cognition plays an important role, i.e. where outcomes are affected by the agents level of understanding of the game and the beliefs they form about each others understanding.We ask whether and when repeated exposure permits agents to learn

  9. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments.

    Science.gov (United States)

    Kudoh, Hiroshi

    2016-04-01

    Phenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High-resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature-responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC-mediated long-term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short-term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

  10. Improvement of the inlet system for the spray-jet technique for use in spectroscopic studies and molecular deposition

    International Nuclear Information System (INIS)

    Yamada, Toshiki; Shinohara, Hidenori; Mashiko, Shinro

    2006-01-01

    We previously developed a molecular beam apparatus with a spray-jet technique in order to produce a molecular beam of non-volatile molecules in vacuum from the sprayed mist of a sample solution. The apparatus is for use in spectroscopic studies or a means of molecular deposition. The spray-jet inlet system consisted of an ultrasonic nebulizer, an inlet chamber and a pulsed nozzle. In the present paper, further improvements to the spray-jet inlet system are reported. The main improvement is the introduction of a pneumatic nebulizer to replace the previous ultrasonic nebulizer. The efficiency of molecular beam generation was evaluated on the basis of the signal intensity of the resonantly enhanced multiphoton ionization time-of-flight mass (REMPI-TOFMS) spectra for a Rhodamine B/methanol solution and the amount of sample consumed. The introduction of the pneumatic nebulizer increased the efficiency by a factor of 20

  11. Performance characteristics of dedicated molecular breast imaging systems at low doses

    Energy Technology Data Exchange (ETDEWEB)

    Long, Zaiyang; Conners, Amy L.; Hunt, Katie N.; Hruska, Carrie B.; O’Connor, Michael K., E-mail: mkoconnor@mayo.edu [Department of Radiology, Mayo Clinic, Rochester, Minnesota 55905 (United States)

    2016-06-15

    Purpose: The purpose of this study was to compare the system performance characteristics and lesion detection capability of two molecular breast imaging (MBI) systems: a multicrystal sodium iodide (NaI)-based single-head system and a cadmium zinc telluride (CZT)-based dual-head system at low administered doses (150–300 MBq) of Tc-99m sestamibi. Methods: System performance characteristics including count sensitivity, uniformity, energy resolution, and spatial resolution were measured using standard NEMA methods, or a modified version thereof in cases where the standard NEMA protocol could not be applied. A contrast-detail phantom with 48 lesions at varying depths from the collimator surface was used to assess lesion contrast-to-noise-ratio (CNR) using background count densities comparable to those observed in patient studies performed with administered doses of 150 MBq Tc-99m sestamibi. Lesions with CNR >3 were deemed to be detectable. Thirty patients undergoing MBI examinations with administered doses of 150–300 MBq were scanned for an additional view on the pixelated NaI system. CNR was calculated for lesions observed on patient images. Background count densities of patient images were measured and compared between the two systems. Results: Over the central field of view, integral and differential uniformity were 6.1% and 4.2%, respectively, for the pixelated NaI system, and 3.8% and 2.7%, respectively, for the CZT system. Count sensitivity was 10.8 kcts/min/MBq for the NaI system and 32.9 kcts/min/MBq for the CZT system. Energy resolution was 13.5% on the pixelated NaI system and 4.5% on the CZT system. Spatial resolution (full-width at half-maximum) for the pixelated NaI detector was 4.2 mm at a distance of 1.2 cm from the collimator and 5.2 mm at 3.1 cm. Spatial resolution of a single CZT detector was 2.9 mm at a distance of 1.2 cm from the collimator and 4.7 mm at 3.1 cm. Effective spatial resolution obtained with dual-head CZT was below 4.7 mm throughout

  12. Endogenous Molecular-Cellular Network Cancer Theory: A Systems Biology Approach.

    Science.gov (United States)

    Wang, Gaowei; Yuan, Ruoshi; Zhu, Xiaomei; Ao, Ping

    2018-01-01

    In light of ever apparent limitation of the current dominant cancer mutation theory, a quantitative hypothesis for cancer genesis and progression, endogenous molecular-cellular network hypothesis has been proposed from the systems biology perspective, now for more than 10 years. It was intended to include both the genetic and epigenetic causes to understand cancer. Its development enters the stage of meaningful interaction with experimental and clinical data and the limitation of the traditional cancer mutation theory becomes more evident. Under this endogenous network hypothesis, we established a core working network of hepatocellular carcinoma (HCC) according to the hypothesis and quantified the working network by a nonlinear dynamical system. We showed that the two stable states of the working network reproduce the main known features of normal liver and HCC at both the modular and molecular levels. Using endogenous network hypothesis and validated working network, we explored genetic mutation pattern in cancer and potential strategies to cure or relieve HCC from a totally new perspective. Patterns of genetic mutations have been traditionally analyzed by posteriori statistical association approaches in light of traditional cancer mutation theory. One may wonder the possibility of a priori determination of any mutation regularity. Here, we found that based on the endogenous network theory the features of genetic mutations in cancers may be predicted without any prior knowledge of mutation propensities. Normal hepatocyte and cancerous hepatocyte stable states, specified by distinct patterns of expressions or activities of proteins in the network, provide means to directly identify a set of most probable genetic mutations and their effects in HCC. As the key proteins and main interactions in the network are conserved through cell types in an organism, similar mutational features may also be found in other cancers. This analysis yielded straightforward and testable

  13. The cobas® 6800/8800 System: a new era of automation in molecular diagnostics.

    Science.gov (United States)

    Cobb, Bryan; Simon, Christian O; Stramer, Susan L; Body, Barbara; Mitchell, P Shawn; Reisch, Natasa; Stevens, Wendy; Carmona, Sergio; Katz, Louis; Will, Stephen; Liesenfeld, Oliver

    2017-02-01

    Molecular diagnostics is a key component of laboratory medicine. Here, the authors review key triggers of ever-increasing automation in nucleic acid amplification testing (NAAT) with a focus on specific automated Polymerase Chain Reaction (PCR) testing and platforms such as the recently launched cobas® 6800 and cobas® 8800 Systems. The benefits of such automation for different stakeholders including patients, clinicians, laboratory personnel, hospital administrators, payers, and manufacturers are described. Areas Covered: The authors describe how molecular diagnostics has achieved total laboratory automation over time, rivaling clinical chemistry to significantly improve testing efficiency. Finally, the authors discuss how advances in automation decrease the development time for new tests enabling clinicians to more readily provide test results. Expert Commentary: The advancements described enable complete diagnostic solutions whereby specific test results can be combined with relevant patient data sets to allow healthcare providers to deliver comprehensive clinical recommendations in multiple fields ranging from infectious disease to outbreak management and blood safety solutions.

  14. New developments in neutron scattering for the study of molecular systems: structure and diffusive motions

    International Nuclear Information System (INIS)

    Volino, F.

    1976-01-01

    After a short review of the main concepts concerning the neutron and its interaction with matter, the authors focus their attention on the study of molecular systems by means of neutron scattering. Instead of reviewing the subject yet again, they limit themselves to the new kind of work which can be done now, with the combined help of high flux reactors and novel instruments. As examples, a few experiments performed at the Institut Laue-Langevin in Grenoble are described: a neutron diffraction study of liquid acetonitrile using a powder diffractometer installed at the hot source; three high-resolution quasi-elastic studies of molecular motions - in an organic solid, (PAA), an organic liquid (C 3 H 6 ) and a liquid crystal (TBBA) - made by combining measurements with high and ultra-high energy resolution spectrometers installed at the cold source. The concept of elastic incoherent structure factor (EISF) is extensively used for the analysis. Finally some prospects on possible future developments are presented. (orig./HK) [de

  15. Analysis of quasielastic neutron scattering (QENS) data of discotic systems using different molecular dynamics (MD) models

    International Nuclear Information System (INIS)

    Kruglova, O.; Mulder, F.M.; Picken, S.J.; Stride, J.; Kearley, G.J.

    2004-01-01

    Discotic molecules are composed of an aromatic core surrounded by aliphatic chains. These molecules are of importance because they can form columns in which the π orbitals of neighbouring molecules overlap leading to conductivity along the column. These materials find applications in molecular electronics and recently--with record quantum efficiencies--in photo voltaics. Because the correlation time of the electron (or hole) hopping is in the picosecond region, molecular dynamics on this timescale is of central importance. We have recently shown that these dynamics, which is easily measured by quasielastic neutron scattering (QENS), can be understood with a rather simple 'short single-column' model via an MD simulation that reproduces the measured QENS spectra. Before progressing to the larger technologically important systems we must understand any fortuitous error cancellations that may cause the simple model to reproduce the experimental signal so well. By taking a very simple discotic, hexamethyltriphenylene (HMT), we are able to compare QENS data with three types of models: simple column, cluster and periodic. It transpires that the cluster model cannot properly accommodate inter column interactions, and a fairly modest periodic model overcomes this problem and the tendency for un-physical harmonic modes along the column

  16. Inhaled Pollutants: The Molecular Scene behind Respiratory and Systemic Diseases Associated with Ultrafine Particulate Matter

    Directory of Open Access Journals (Sweden)

    Hussein Traboulsi

    2017-01-01

    Full Text Available Air pollution of anthropogenic origin is largely from the combustion of biomass (e.g., wood, fossil fuels (e.g., cars and trucks, incinerators, landfills, agricultural activities and tobacco smoke. Air pollution is a complex mixture that varies in space and time, and contains hundreds of compounds including volatile organic compounds (e.g., benzene, metals, sulphur and nitrogen oxides, ozone and particulate matter (PM. PM0.1 (ultrafine particles (UFP, those particles with a diameter less than 100 nm (includes nanoparticles (NP are considered especially dangerous to human health and may contribute significantly to the development of numerous respiratory and cardiovascular diseases such as chronic obstructive pulmonary disease (COPD and atherosclerosis. Some of the pathogenic mechanisms through which PM0.1 may contribute to chronic disease is their ability to induce inflammation, oxidative stress and cell death by molecular mechanisms that include transcription factors such as nuclear factor κB (NF-κB and nuclear factor (erythroid-derived 2-like 2 (Nrf2. Epigenetic mechanisms including non-coding RNA (ncRNA may also contribute towards the development of chronic disease associated with exposure to PM0.1. This paper highlights emerging molecular concepts associated with inhalational exposure to PM0.1 and their ability to contribute to chronic respiratory and systemic disease.

  17. Molecular finite-size effects in stochastic models of equilibrium chemical systems.

    Science.gov (United States)

    Cianci, Claudia; Smith, Stephen; Grima, Ramon

    2016-02-28

    The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here, we introduce the excluded volume reaction-diffusion master equation (vRDME) which takes into account volume exclusion effects on stochastic kinetics due to a finite molecular radius. We obtain an exact closed form solution of the RDME and of the vRDME for a general chemical system in equilibrium conditions. The difference between the two solutions increases with the ratio of molecular diameter to the compartment length scale. We show that an increase in the fraction of excluded space can (i) lead to deviations from the classical inverse square root law for the noise-strength, (ii) flip the skewness of the probability distribution from right to left-skewed, (iii) shift the equilibrium of bimolecular reactions so that more product molecules are formed, and (iv) strongly modulate the Fano factors and coefficients of variation. These volume exclusion effects are found to be particularly pronounced for chemical species not involved in chemical conservation laws. Finally, we show that statistics obtained using the vRDME are in good agreement with those obtained from Brownian dynamics with excluded volume interactions.

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

    Science.gov (United States)

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

    2018-02-01

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

  19. Colorimetric test-systems for creatinine detection based on composite molecularly imprinted polymer membranes.

    Science.gov (United States)

    Sergeyeva, T A; Gorbach, L A; Piletska, E V; Piletsky, S A; Brovko, O O; Honcharova, L A; Lutsyk, O D; Sergeeva, L M; Zinchenko, O A; El'skaya, A V

    2013-04-03

    An easy-to-use colorimetric test-system for the efficient detection of creatinine in aqueous samples was developed. The test-system is based on composite molecularly imprinted polymer (MIP) membranes with artificial receptor sites capable of creatinine recognition. A thin MIP layer was created on the surface of microfiltration polyvinylidene fluoride (PVDF) membranes using method of photo-initiated grafting polymerization. The MIP layer was obtained by co-polymerization of a functional monomer (e.g. 2-acrylamido-2-methyl-1-propanesulfonic acid, itaconic acid or methacrylic acid) with N, N'-methylenebisacrylamide as a cross-linker. The choice of the functional monomer was based on the results of computational modeling. The creatinine-selective composite MIP membranes were used for measuring creatinine in aqueous samples. Creatinine molecules were selectively adsorbed by the MIP membranes and quantified using color reaction with picrates. The intensity of MIP membranes staining was proportional to creatinine concentration in an analyzed sample. The colorimetric test-system based on the composite MIP membranes was characterized with 0.25 mM detection limit and 0.25-2.5mM linear dynamic range. Storage stability of the MIP membranes was estimated as at least 1 year at room temperature. As compared to the traditional methods of creatinine detection the developed test-system is characterized by simplicity of operation, small size and low cost. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

    KAUST Repository

    Watanabe, H.

    2011-08-01

    Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatialdecomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.

  1. Artificial liver support with the molecular adsorbent recirculating system: activation of coagulation and bleeding complications.

    Science.gov (United States)

    Bachli, Esther B; Schuepbach, Reto A; Maggiorini, Marco; Stocker, Reto; Müllhaupt, Beat; Renner, Eberhard L

    2007-05-01

    Numerous, mostly uncontrolled, observations suggest that artificial liver support with the Molecular Adsorbent Recirculating System (MARS) improves pathophysiologic sequelae and outcome of acute and acute-on-chronic liver failure. MARS is felt to be safe, but extracorporeal circuits may activate coagulation. To assess the frequency of and risk factors for activation of coagulation during MARS treatment. Retrospective analysis of coagulopathy/bleeding complications observed during 83 consecutive MARS sessions in 21 patients (11 men; median age 46 years; median three sessions per patient; median duration of session 8 h). Nine clinically relevant episodes of coagulopathy/bleeding were observed in eight patients, forced to premature cessation of MARS in seven and ended lethal in four. Four complications occurred during the first, five during later (third to seventh) MARS sessions and two bleeders tolerated further sessions without complications. Coagulation parameters worsened significantly also during MARS sessions not associated with bleeding (PMARS therapy, potentially leading to bleeding complications and mortality.

  2. Optimization and performance evaluation of a conical mirror based fluorescence molecular tomography imaging system

    Science.gov (United States)

    Zhao, Yue; Zhang, Wei; Zhu, Dianwen; Li, Changqing

    2016-03-01

    We performed numerical simulations and phantom experiments with a conical mirror based fluorescence molecular tomography (FMT) imaging system to optimize its performance. With phantom experiments, we have compared three measurement modes in FMT: the whole surface measurement mode, the transmission mode, and the reflection mode. Our results indicated that the whole surface measurement mode performed the best. Then, we applied two different neutral density (ND) filters to improve the measurement's dynamic range. The benefits from ND filters are not as much as predicted. Finally, with numerical simulations, we have compared two laser excitation patterns: line and point. With the same excitation position number, we found that the line laser excitation had slightly better FMT reconstruction results than the point laser excitation. In the future, we will implement Monte Carlo ray tracing simulations to calculate multiple reflection photons, and create a look-up table accordingly for calibration.

  3. Possible signatures of nuclear-molecular formation in O+C systems

    International Nuclear Information System (INIS)

    Tighe, R.J.; Kolata, J.J.; Belbot, M.; Aguilera, E.F.

    1993-01-01

    The interplay between the elastic, quasielastic, and fusion reaction channels at energies from just above to well below the Coulomb barrier is investigated for O+C systems. Elastic-scattering and quasielastic-scattering angular distributions were measured using the kinematic coincidence technique. Fusion yields were obtained by direct detection of the evaporation residues using a time-of-flight energy spectrometer, at energies from just above to well below the Coulomb barrier. The fusion yields differ significantly from previous work, but the present measurements give barrier parameters consistent with systematics. Comparisons with two-center shell model and coupled-channels predictions show possible indications of nuclear-molecular formation in the elastic, inelastic, and single-neutron transfer channels

  4. Acidolysis small molecular phenolic ether used as accelerator in photosensitive diazonaphthaquinone systems

    Science.gov (United States)

    Zhou, Haihua; Zou, Yingquan

    2006-03-01

    The photosensitive compounds in the photosensitive coatings of positive PS plates are the diazonaphthaquinone derivatives. Some acidolysis small molecular phenolic ethers, which were synthesized by some special polyhydroxyl phenols with vinyl ethyl ether, are added in the positive diazonaphthaquinone photosensitive composition to improve its sensitivity, composed with photo-acid-generators. The effects to the photosensitivity, anti-alkali property, anti-isopropyl alcohol property, dot resolution and line resolution of the coatings are studied with different additive percent of the special phenolic ethers. In the conventional photosensitive diazonaphthaquinone systems for positive PS plates, the photosensitivity is improved without negative effects to resolution, anti-alkali and anti-isopropyl alcohol properties when added about 5% of the special acidolysis phenolic ethers, EAAE or DPHE, composed with photo-acid-generators.

  5. First Principles Molecular Dynamics Study of Catalysis for Polyolefins: the Ziegler-Natta Heterogeneous System.

    Directory of Open Access Journals (Sweden)

    Michele Parrinello

    2002-04-01

    Full Text Available Abstract: We review part of our recent ab initio molecular dynamics study on the Ti-based Ziegler-Natta supported heterogeneous catalysis of α-olefins. The results for the insertion of ethylene in the metal-carbon bond are discussed as a fundamental textbook example of polymerization processes. Comparison with the few experimental data available has shown that simulation can reproduce activation barriers and the overall energetics of the reaction with sufficient accuracy. This puts these quantum dynamical simulations in a new perspective as a virtual laboratory where the microscopic picture of the catalysis, which represents an important issue that still escapes experimental probes, can be observed and understood. These results are then discussed in comparison with a V-based catalyst in order to figure out analogies and differences with respect to the industrially more successful Tibased systems.

  6. Molecular dynamics simulations of Na+/Cl--dependent neurotransmitter transporters in a membrane-aqueous system

    DEFF Research Database (Denmark)

    Jørgensen, Anne Marie; Tagmose, L.; Jørgensen, A.M.M.

    2007-01-01

    We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate S-HT or the selective serotonin reuptake inhibitor escitaloprom. We have also included a transporter homologue......, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystal logrophic B factors. Furthermore, key interactions identified in the X....... Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitaloprom complexes. Our finding5 are in good agreement with predictions from mutagenesis studies....

  7. Enhancement of phase-conjugate reflectivity using Zeeman coherence in highly degenerate molecular systems

    International Nuclear Information System (INIS)

    Mukherjee, Nandini

    2010-01-01

    A comprehensive theoretical analysis is developed for the vectorial phase conjugation using resonant four-wave mixing (FWM) in a highly degenerate rotational vibrational molecular system. The dynamic Stark shifts, saturation, and Doppler broadening are included for a realistic analysis. It is shown that the electromagnetically induced multilevel coherence controls the nonlinear wave mixing yielding interesting results for the phase conjugate (PC) reflectivity. It turns out that the efficiency of the PC reflectivity is decided by the relative phase of the Zeeman coherence and the population grating. When these two contributions are aligned in phase by a small detuning of the pump frequency, a large PC reflectivity (∼20%) is obtained with moderate pump intensity (∼500 mW/cm 2 ).

  8. Simple Rules for an Efficient Use of Geographic Information Systems in Molecular Ecology

    Directory of Open Access Journals (Sweden)

    Kevin Leempoel

    2017-04-01

    Full Text Available Geographic Information Systems (GIS are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA. This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages.

  9. Highly ordered self-assembly of one-dimensional nanoparticles in amphiphilic molecular systems

    International Nuclear Information System (INIS)

    Kim, Tae Hwan

    2009-02-01

    Two kinds of one-dimensional (1D) nanoparticles, stable rod-like nanoparticles with highly controlled surface charge density (cROD) and non-covalently functionalized isolated single wall carbon nanotubes (p-SWNT) that were readily redispersible in water, have been developed. Using these 1D nanoparticles, various highly ordered superstructures of 1D nanoparticles by molecular self-assembling based on electrostatic interaction in amphiphilic molecular systems (two different cationic liposome systems) have been investigated. To our knowledge, this is the first demonstration of highly ordered self-assembly of 1D nanoparticles based on electrostatic interaction between 1D nanoparticles and amphiphilic molecules. The cRODs have been developed by free radical polymerization of a mixture of polymerizable cationic surfactant, cetyltrimethylammonium 4-vinylbenzoate (CTVB), and hydrotropic salt sodium 4-styrenesulfonate (NaSS) in aqueous solution. The surface charge of the cROD was controlled by varying the NaSS concentration during the polymerization process and the charge variation was interpreted in terms of the overcharging effect in colloidal systems. The small angle neutron scattering (SANS) measurements showed that the diameter of cROD is constant at 4 nm and the particle length ranges from 20 nm to 85 nm, depending on the NaSS concentration. The cRODs are longest when the NaSS concentration is 5 mol % which corresponds to the charge inversion or neutral point. The SANS and zeta potential measurements showed that the Coulomb interactions between the particles are strongly dependent on the NaSS concentration and the zeta potential of the cRODs changes from positive to negative (+ 12.8 mV ∼ - 44.2 mV) as the concentration of NaSS increases from 0 mol % to 40 mol %. As the NaSS concentration is further increased, the zeta potential is saturated at approximately - 50 mV. The p-SWNTs have been developed by 1) dispersing single wall carbon nanotubes (SWNTs) in water using

  10. Homeostasis-altering molecular processes as mechanisms of inflammasome activation.

    Science.gov (United States)

    Liston, Adrian; Masters, Seth L

    2017-03-01

    The innate immune system uses a distinct set of germline-encoded pattern recognition receptors (PRRs) to initiate downstream inflammatory cascades. This recognition system is in stark contrast to the adaptive immune system, which relies on highly variable, randomly generated antigen receptors. A key limitation of the innate immune system's reliance on fixed PRRs is its inflexibility in responding to rapidly evolving pathogens. Recent advances in our understanding of inflammasome activation suggest that the innate immune system also has sophisticated mechanisms for responding to pathogens for which there is no fixed PRR. This includes the recognition of debris from dying cells, known as danger-associated molecular patterns (DAMPs), which can directly activate PRRs in a similar manner to pathogen-associated molecular patterns (PAMPs). Distinct from this, emerging data for the inflammasome components NLRP3 (NOD-, LRR- and pyrin domain-containing 3) and pyrin suggest that they do not directly detect molecular patterns, but instead act as signal integrators that are capable of detecting perturbations in cytoplasmic homeostasis, for example, as initiated by infection. Monitoring these perturbations, which we term 'homeostasis-altering molecular processes' (HAMPs), provides potent flexibility in the capacity of the innate immune system to detect evolutionarily novel infections; however, HAMP sensing may also underlie the sterile inflammation that drives chronic inflammatory diseases.

  11. Long-range force and moment calculations in multiresolution simulations of molecular systems

    International Nuclear Information System (INIS)

    Poursina, Mohammad; Anderson, Kurt S.

    2012-01-01

    Multiresolution simulations of molecular systems such as DNAs, RNAs, and proteins are implemented using models with different resolutions ranging from a fully atomistic model to coarse-grained molecules, or even to continuum level system descriptions. For such simulations, pairwise force calculation is a serious bottleneck which can impose a prohibitive amount of computational load on the simulation if not performed wisely. Herein, we approximate the resultant force due to long-range particle-body and body-body interactions applicable to multiresolution simulations. Since the resultant force does not necessarily act through the center of mass of the body, it creates a moment about the mass center. Although this potentially important torque is neglected in many coarse-grained models which only use particle dynamics to formulate the dynamics of the system, it should be calculated and used when coarse-grained simulations are performed in a multibody scheme. Herein, the approximation for this moment due to far-field particle-body and body-body interactions is also provided.

  12. Enzymatic logic calculation systems based on solid-state electrochemiluminescence and molecularly imprinted polymer film electrodes.

    Science.gov (United States)

    Lian, Wenjing; Liang, Jiying; Shen, Li; Jin, Yue; Liu, Hongyun

    2018-02-15

    The molecularly imprinted polymer (MIP) films were electropolymerized on the surface of Au electrodes with luminol and pyrrole (PY) as the two monomers and ampicillin (AM) as the template molecule. The electrochemiluminescence (ECL) intensity peak of polyluminol (PL) of the AM-free MIP films at 0.7V vs Ag/AgCl could be greatly enhanced by AM rebinding. In addition, the ECL signals of the MIP films could also be enhanced by the addition of glucose oxidase (GOD)/glucose and/or ferrocenedicarboxylic acid (Fc(COOH) 2 ) in the testing solution. Moreover, Fc(COOH) 2 exhibited cyclic voltammetric (CV) response at the AM-free MIP film electrodes. Based on these results, a binary 3-input/6-output biomolecular logic gate system was established with AM, GOD and Fc(COOH) 2 as inputs and the ECL responses at different levels and CV signal as outputs. Some functional non-Boolean logic devices such as an encoder, a decoder and a demultiplexer were also constructed on the same platform. Particularly, on the basis of the same system, a ternary AND logic gate was established. The present work combined MIP film electrodes, the solid-state ECL, and the enzymatic reaction together, and various types of biomolecular logic circuits and devices were developed, which opened a novel avenue to construct more complicated bio-logic gate systems. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Advances in Molecular Imaging of Locally Delivered Targeted Therapeutics for Central Nervous System Tumors

    Directory of Open Access Journals (Sweden)

    Umberto Tosi

    2017-02-01

    Full Text Available Thanks to the recent advances in the development of chemotherapeutics, the morbidity and mortality of many cancers has decreased significantly. However, compared to oncology in general, the field of neuro-oncology has lagged behind. While new molecularly targeted chemotherapeutics have emerged, the impermeability of the blood–brain barrier (BBB renders systemic delivery of these clinical agents suboptimal. To circumvent the BBB, novel routes of administration are being applied in the clinic, ranging from intra-arterial infusion and direct infusion into the target tissue (convection enhanced delivery (CED to the use of focused ultrasound to temporarily disrupt the BBB. However, the current system depends on a “wait-and-see” approach, whereby drug delivery is deemed successful only when a specific clinical outcome is observed. The shortcomings of this approach are evident, as a failed delivery that needs immediate refinement cannot be observed and corrected. In response to this problem, new theranostic agents, compounds with both imaging and therapeutic potential, are being developed, paving the way for improved and monitored delivery to central nervous system (CNS malignancies. In this review, we focus on the advances and the challenges to improve early cancer detection, selection of targeted therapy, and evaluation of therapeutic efficacy, brought forth by the development of these new agents.

  14. Reinforced dynamics for enhanced sampling in large atomic and molecular systems

    Science.gov (United States)

    Zhang, Linfeng; Wang, Han; E, Weinan

    2018-03-01

    A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. The method is illustrated by studying the full-atom explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables.

  15. Micelle System Based on Molecular Economy Principle for Overcoming Multidrug Resistance and Inhibiting Metastasis.

    Science.gov (United States)

    Qi, Yan; Qin, Xianya; Yang, Conglian; Wu, Tingting; Qiao, Qi; Song, Qingle; Zhang, Zhiping

    2018-03-05

    The high mortality of cancer is mainly attributed to multidrug resistance (MDR) and metastasis. A simple micelle system was constructed here to codeliver doxorubicin (DOX), adjudin (ADD), and nitric oxide (NO) for overcoming MDR and inhibiting metastasis. It was devised based on the "molecular economy" principle as the micelle system was easy to fabricate and exhibited high drug loading efficiency, and importantly, each component of the micelles would exert one or more active functions. DOX acted as the main cell killing agent supplemented with ADD, NO, and d-α-tocopheryl polyethylene glycol 1000 succinate (TPGS). MDR was overcome by synergistic effects of mitochondria inhibition agents, TPGS and ADD. A TPGS-based NO donor can be used as a drug carrier, and it can release NO to enhance drug accumulation and penetration in tumor, resulting in a positive cycle of drug delivery. This DOX-ADD conjugate self-assembly system demonstrated controlled drug release, increased cellular uptake and cytotoxicity, enhanced accumulation at tumor site, and improved in vivo metastasis inhibition of breast cancer. The micelles can fully take advantage of the functions of each component, and they provide a potential strategy for nanomedicine design and clinical cancer treatment.

  16. Advances in Molecular Imaging of Locally Delivered Targeted Therapeutics for Central Nervous System Tumors

    Science.gov (United States)

    Tosi, Umberto; Marnell, Christopher S.; Chang, Raymond; Cho, William C.; Ting, Richard; Maachani, Uday B.; Souweidane, Mark M.

    2017-01-01

    Thanks to the recent advances in the development of chemotherapeutics, the morbidity and mortality of many cancers has decreased significantly. However, compared to oncology in general, the field of neuro-oncology has lagged behind. While new molecularly targeted chemotherapeutics have emerged, the impermeability of the blood–brain barrier (BBB) renders systemic delivery of these clinical agents suboptimal. To circumvent the BBB, novel routes of administration are being applied in the clinic, ranging from intra-arterial infusion and direct infusion into the target tissue (convection enhanced delivery (CED)) to the use of focused ultrasound to temporarily disrupt the BBB. However, the current system depends on a “wait-and-see” approach, whereby drug delivery is deemed successful only when a specific clinical outcome is observed. The shortcomings of this approach are evident, as a failed delivery that needs immediate refinement cannot be observed and corrected. In response to this problem, new theranostic agents, compounds with both imaging and therapeutic potential, are being developed, paving the way for improved and monitored delivery to central nervous system (CNS) malignancies. In this review, we focus on the advances and the challenges to improve early cancer detection, selection of targeted therapy, and evaluation of therapeutic efficacy, brought forth by the development of these new agents. PMID:28208698

  17. Electromagnetically induced transparency in an open V-type molecular system

    International Nuclear Information System (INIS)

    Lazoudis, A.; Ahmed, E. H.; Qi, P.; Lyyra, A. M.; Kirova, T.; Huennekens, J.

    2011-01-01

    We report the experimental observation of electromagnetically induced transparency (EIT) in an inhomogeneously broadened V-type Na 2 molecular system. The experiment is performed with both co- and counterpropagating arrangements for the propagation directions of the coupling and probe laser beams. In our theoretical model we employ the density matrix formalism, as well as perturbative methods for obtaining the probe field absorption profile for both open and closed systems. Simulations of the experimental data show excellent agreement with the predictions derived from the basic theory. Our fluorescent intensity measurements show that, in the copropagating configuration, the EIT plus saturation window depth is about 95%, while under similar conditions in the counterpropagating geometry we observed 40%-45% reduction in the fluorescence signal around the line center. To separate the two simultaneously occurring mechanisms in a V-type system (i.e., EIT and saturation) that are induced by the coupling field, we have carried out theoretical calculations which show that, in the copropagating case, a significant fraction of the depth of the dip is due to the coherent effect of EIT. When the coupling and probe beams are in the counterpropagating configuration, the dip is mostly due to saturation effects alone.

  18. Molecular system analysis, multidimensional, dynamic, ultra-sensitive exploration of proteomes

    International Nuclear Information System (INIS)

    Scharattenholz, A.; Soski, V.; Stegmann, W.; Schroer, K.; Godovac-Zimmermann, J.; Cabuk, A.; Pejovi, V.; Wozny, W.; Cahill, M.A.; Drukier, A.K.; Volkovitsky, P.

    2001-01-01

    ProteoSys AG's holistic proteomics strategy extends beyond classical proteome research as a new paradigm. Our concept of multidimensional molecular systems analysis of complex model systems employs the innovative ProteoDyn TM approach. This enables us to correlate dynamic changes of proteomes with their biophysical and biochemical environment. Our supersensitive Multi Photon Detection (MPD) technology enables ultra-sensitive detection of proteins, deep into the low abundance domain. Our technology platform includes the affinity analysis of phospho- and glyco-proteomes, and with our 'fish hook' methods we can capture and fully characterize even serpentine G-coupled receptors and associated proteins, including routine comprehensive post-translational analyses performed by a well equipped mass spectrometry group. Throughput and quality is obtained by automation and high end robotics, with data management handled by a dedicated bioinformatics department. Thus ProteoSys AG has a range of state of the art and proprietary tools at its disposal to analyse even the most difficult complex model systems. MPD is an isotopic detection method proprietary to ProteoSys For MPD analysis we have implemented protocols where over 99% of proteins can be iodinated, and where the iodinated proteins can be identified by mass spectrometry. Because MPD measures the energy of detected particles, it can discriminate between signals originating from different isotopes co-electrophoresed by 2D-PAGE. Thus MPD imagers have a 'multicolour' functionality suitable for differential display and improved throughput, eliminating inter-gel variations. Importantly, MPD opens up not only the world of detection of low abundance proteins, but also identification and characterization. Radioactive low abundance protein spots containing less than one attomole of protein can be excised from a 2D-gel, mixed with unlabelled proteins, and 'tracked' by MPD. The identity of the labeled protein is determined by

  19. Molecular basis of Trypanosoma cruzi and Leishmania interaction with their host(s): exploitation of immune and defense mechanisms by the parasite leading to persistence and chronicity, features reminiscent of immune system evasion strategies in cancer diseases.

    Science.gov (United States)

    Ouaissi, Ali; Ouaissi, Mehdi

    2005-01-01

    A number of features occurring during host-parasite interactions in Chagas disease caused by the protozoan parasite, Trypanosoma cruzi, and Leishmaniasis, caused by a group of kinetoplastid protozoan parasites are reminiscent of those observed in cancer diseases. In fact,although the cancer is not a single disease, and that T.cruzi and Leishmania are sophisticated eukaryotic parasites presenting a high level of genotypic variability the growth of the parasites in their host and that of cancer cells share at least one common feature, that is their mutual capacity for rapid cell division. Surprisingly, the parasitic diseases and cancers share some immune evasion strategies. Consideration of these immunological alterations must be added to the evaluation of the pathogenic processes. The molecular and functional characterization of virulence factors and the study of their effect on the arms of the immune system have greatly improved understanding of the regulation of immune effectors functions. The purpose of this review is to analyze some of the current data related to the regulatory components or processes originating from the parasite that control or interfere with host cell physiology. Attempts are also made to delineate some similarities between the immune evasion strategies that parasites and tumors employ. The elucidation of the mode of action of parasite virulence factors toward the host cell allow not only provide us with a more comprehensive view of the host-parasite relationships but may also represent a step forward in efforts aimed to identify new target molecules for therapeutic intervention.

  20. Expanding the molecular toolbox for Lactococcus lactis: construction of an inducible thioredoxin gene fusion expression system

    LENUS (Irish Health Repository)

    Douillard, Francois P

    2011-08-09

    Abstract Background The development of the Nisin Inducible Controlled Expression (NICE) system in the food-grade bacterium Lactococcus lactis subsp. cremoris represents a cornerstone in the use of Gram-positive bacterial expression systems for biotechnological purposes. However, proteins that are subjected to such over-expression in L. lactis may suffer from improper folding, inclusion body formation and\\/or protein degradation, thereby significantly reducing the yield of soluble target protein. Although such drawbacks are not specific to L. lactis, no molecular tools have been developed to prevent or circumvent these recurrent problems of protein expression in L. lactis. Results Mimicking thioredoxin gene fusion systems available for E. coli, two nisin-inducible expression vectors were constructed to over-produce various proteins in L. lactis as thioredoxin fusion proteins. In this study, we demonstrate that our novel L. lactis fusion partner expression vectors allow high-level expression of soluble heterologous proteins Tuc2009 ORF40, Bbr_0140 and Tuc2009 BppU\\/BppL that were previously insoluble or not expressed using existing L. lactis expression vectors. Over-expressed proteins were subsequently purified by Ni-TED affinity chromatography. Intact heterologous proteins were detected by immunoblotting analyses. We also show that the thioredoxin moiety of the purified fusion protein was specifically and efficiently cleaved off by enterokinase treatment. Conclusions This study is the first description of a thioredoxin gene fusion expression system, purposely developed to circumvent problems associated with protein over-expression in L. lactis. It was shown to prevent protein insolubility and degradation, allowing sufficient production of soluble proteins for further structural and functional characterization.

  1. Peptide and low molecular weight proteins based kidney targeted drug delivery systems.

    Science.gov (United States)

    Xu, Pengfei; Zhang, Hailiang; Dang, Ruili; Jiang, Pei

    2018-05-30

    Renal disease is a worldwide public health problem, and unfortunately, the therapeutic index of regular drugs is limited. Thus, it is a great need to develop effective treatment strategies. Among the reported strategies, kidney-targeted drug delivery system is a promising method to increase renal efficacy and reduce extra-renal toxicity. In recent years, working as vehicles for targeted drug delivery, low molecular weight proteins (LMWP) and peptide have received immense attention due to their many advantages, such as selective accumulation in kidney, high drug loading capability, control over routes of biodegradation, convenience in modification at the amino terminus, and good biocompatibility. In this review, we describe the current LMWP and peptide carriers for kidney targeted drug delivery systems. In addition, we discuss different linking strategies between carriers and drugs. Furthermore, we briefly outline the current status and attempt to give an outlook on the further study. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  2. Fast Batch Production of High-Quality Graphene Films in a Sealed Thermal Molecular Movement System.

    Science.gov (United States)

    Xu, Jianbao; Hu, Junxiong; Li, Qi; Wang, Rubing; Li, Weiwei; Guo, Yufen; Zhu, Yongbo; Liu, Fengkui; Ullah, Zaka; Dong, Guocai; Zeng, Zhongming; Liu, Liwei

    2017-07-01

    Chemical vapor deposition (CVD) growth of high-quality graphene has emerged as the most promising technique in terms of its integrated manufacturing. However, there lacks a controllable growth method for producing high-quality and a large-quantity graphene films, simultaneously, at a fast growth rate, regardless of roll-to-roll (R2R) or batch-to-batch (B2B) methods. Here, a stationary-atmospheric-pressure CVD (SAPCVD) system based on thermal molecular movement, which enables fast B2B growth of continuous and uniform graphene films on tens of stacked Cu(111) foils, with a growth rate of 1.5 µm s -1 , is demonstrated. The monolayer graphene of batch production is found to nucleate from arrays of well-aligned domains, and the films possess few defects and exhibit high carrier mobility up to 6944 cm 2 V -1 s -1 at room temperature. The results indicate that the SAPCVD system combined with single-domain Cu(111) substrates makes it possible to realize fast batch-growth of high-quality graphene films, which opens up enormous opportunities to use this unique 2D material for industrial device applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Molecular System Dynamics for Self-Organization in Heterogeneous Wireless Networks

    Directory of Open Access Journals (Sweden)

    Milner StuartD

    2010-01-01

    Full Text Available We have been looking at the properties of physical configurations that occur in nature in order to characterize, predict, and control network robustness in dynamic communication networks. Our framework is based on the definition of a potential energy function to characterize robustness in communication networks and the study of first- and second-order variations of the potential energy to provide prediction and control strategies for network-performance optimization. This paper describes novel investigations within this framework that draw from molecular system dynamics. The Morse potential, which governs the energy stored in bonds within molecules, is considered for the characterization of the potential energy of communication links in the presence of physical constraints such as the power available at the transmitters in a network. The inclusion of the Morse potential translates into improved control strategies, where forces on network nodes drive the release, retention, or reconfiguration of communication links based on their role within the network architecture. The performance of the proposed approach is measured in terms of the number of source-to-destination connections that have an end-to-end communications path. Simulation results show the effectiveness of our control mechanism, where the physical topology reorganizes to maximize the number of source-to-destination communicating pairs. The algorithms developed are completely distributed, show constant time complexity and produce optimal solutions from local interactions, thus preserving the system's self-organizing capability.

  4. Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System.

    Science.gov (United States)

    Kanofsky, Konstantin; Lehmeyer, Mona; Schulze, Jutta; Hehl, Reinhard

    2016-01-01

    Plants recognize pathogens by microbe-associated molecular patterns (MAMPs) and subsequently induce an immune response. The regulation of gene expression during the immune response depends largely on cis-sequences conserved in promoters of MAMP-responsive genes. These cis-sequences can be analyzed by constructing synthetic promoters linked to a reporter gene and by testing these constructs in transient expression systems. Here, the use of the parsley (Petroselinum crispum) protoplast system for analyzing MAMP-responsive synthetic promoters is described. The synthetic promoter consists of four copies of a potential MAMP-responsive cis-sequence cloned upstream of a minimal promoter and the uidA reporter gene. The reporter plasmid contains a second reporter gene, which is constitutively expressed and hence eliminates the requirement of a second plasmid used as a transformation control. The reporter plasmid is transformed into parsley protoplasts that are elicited by the MAMP Pep25. The MAMP responsiveness is validated by comparing the reporter gene activity from MAMP-treated and untreated cells and by normalizing reporter gene activity using the constitutively expressed reporter gene.

  5. Auxiliary-field quantum Monte Carlo calculations of molecular systems with a Gaussian basis

    International Nuclear Information System (INIS)

    Al-Saidi, W.A.; Zhang Shiwei; Krakauer, Henry

    2006-01-01

    We extend the recently introduced phaseless auxiliary-field quantum Monte Carlo (QMC) approach to any single-particle basis and apply it to molecular systems with Gaussian basis sets. QMC methods in general scale favorably with the system size as a low power. A QMC approach with auxiliary fields, in principle, allows an exact solution of the Schroedinger equation in the chosen basis. However, the well-known sign/phase problem causes the statistical noise to increase exponentially. The phaseless method controls this problem by constraining the paths in the auxiliary-field path integrals with an approximate phase condition that depends on a trial wave function. In the present calculations, the trial wave function is a single Slater determinant from a Hartree-Fock calculation. The calculated all-electron total energies show typical systematic errors of no more than a few millihartrees compared to exact results. At equilibrium geometries in the molecules we studied, this accuracy is roughly comparable to that of coupled cluster with single and double excitations and with noniterative triples [CCSD(T)]. For stretched bonds in H 2 O, our method exhibits a better overall accuracy and a more uniform behavior than CCSD(T)

  6. NATO Advanced Study Institute on Lower-Dimensional Systems and Molecular Electronics

    CERN Document Server

    Day, Peter; Papavassiliou, George

    1990-01-01

    This volume represents the written account of the NATO Advanced Study Institute "Lower-Dimensional Systems and Molecular Electronics" held at Hotel Spetses, Spetses Island, Greece from 12 June to 23 June 1989. The goal of the Institute was to demonstrate the breadth of chemical and physical knowledge that has been acquired in the last 20 years in inorganic and organic crystals, polymers, and thin films, which exhibit phenomena of reduced dimensionality. The interest in these systems started in the late 1960's with lower-dimensional inorganic conductors, in the early 1970's with quasi-one-dimensional crystalline organic conductors. which by 1979 led to the first organic superconductors, and, in 1977, to the fITSt conducting polymers. The study of monolayer films (Langmuir-Blodgett films) had progressed since the 1930's, but reached a great upsurge in . the early 1980's. The pursuit of non-linear optical phenomena became increasingly popular in the early 1980's, as the attention turned from inorganic crystals t...

  7. Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seonghan; Chang, Rakwoo [Kwangwoon University, Seoul (Korea, Republic of)

    2016-07-15

    Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel-like (L{sub β}' or P{sub β}') phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel-like phase into the completely liquid-crystalline phase (L{sub α}). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half-maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness)can be used as order parameters for the membrane phase transition.

  8. Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

    International Nuclear Information System (INIS)

    Kim, Seonghan; Chang, Rakwoo

    2016-01-01

    Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel-like (L_β' or P_β') phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel-like phase into the completely liquid-crystalline phase (L_α). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half-maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness)can be used as order parameters for the membrane phase transition.

  9. Proceedings of the 3. international symposium on applied microbiology and molecular biology in oil systems: ISMOS 3

    Energy Technology Data Exchange (ETDEWEB)

    Rooijen, Gijs van; Caffrey, Sean M. [Genome Alberta (Canada); Lund Skovhus, Torben [DTI Oil and Gas (Denmark); Whitby, Corinne [University of Essex (United Kingdom)

    2011-07-01

    The 3rd international symposium on applied microbiology and molecular biology in oil systems was held in Calgary, Alberta, Canada, from June 13th to June 15th, 2011. This conference, organized by ISMOS TSC, gathered experts to discuss the application of microbial and molecular biology in the hydrocarbon sector. The conference was attended by key players from the oil and gas industry and provided them with the opportunity to learn about some of the latest technologies in areas such as the application of molecular microbiological methods for oil field systems, biodegradation of hydrocarbons in oil production, biofuels and downstream petroleum microbiology and challenges in biofuels and oil sands developments, and to network with their peers and share their expertise. 17 of the 31 papers presented during this conference have been catalogued separately for inclusion in this database.

  10. Effective Brownian ratchet separation by a combination of molecular filtering and a self-spreading lipid bilayer system.

    Science.gov (United States)

    Motegi, Toshinori; Nabika, Hideki; Fu, Yingqiang; Chen, Lili; Sun, Yinlu; Zhao, Jianwei; Murakoshi, Kei

    2014-07-01

    A new molecular manipulation method in the self-spreading lipid bilayer membrane by combining Brownian ratchet and molecular filtering effects is reported. The newly designed ratchet obstacle was developed to effectively separate dye-lipid molecules. The self-spreading lipid bilayer acted as both a molecular transport system and a manipulation medium. By controlling the size and shape of ratchet obstacles, we achieved a significant increase in the separation angle for dye-lipid molecules compared to that with the previous ratchet obstacle. A clear difference was observed between the experimental results and the simple random walk simulation that takes into consideration only the geometrical effect of the ratchet obstacles. This difference was explained by considering an obstacle-dependent local decrease in molecular diffusivity near the obstacles, known as the molecular filtering effect at nanospace. Our experimental findings open up a novel controlling factor in the Brownian ratchet manipulation that allow the efficient separation of molecules in the lipid bilayer based on the combination of Brownian ratchet and molecular filtering effects.

  11. Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics

    Science.gov (United States)

    Puzyrkov, Dmitry; Polyakov, Sergey; Podryga, Viktoriia; Markizov, Sergey

    2018-02-01

    At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.

  12. Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Puzyrkov Dmitry

    2018-01-01

    Full Text Available At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.

  13. Sophisticated approval voting, ignorance priors, and plurality heuristics: a behavioral social choice analysis in a Thurstonian framework.

    Science.gov (United States)

    Regenwetter, Michel; Ho, Moon-Ho R; Tsetlin, Ilia

    2007-10-01

    This project reconciles historically distinct paradigms at the interface between individual and social choice theory, as well as between rational and behavioral decision theory. The authors combine a utility-maximizing prescriptive rule for sophisticated approval voting with the ignorance prior heuristic from behavioral decision research and two types of plurality heuristics to model approval voting behavior. When using a sincere plurality heuristic, voters simplify their decision process by voting for their single favorite candidate. When using a strategic plurality heuristic, voters strategically focus their attention on the 2 front-runners and vote for their preferred candidate among these 2. Using a hierarchy of Thurstonian random utility models, the authors implemented these different decision rules and tested them statistically on 7 real world approval voting elections. They cross-validated their key findings via a psychological Internet experiment. Although a substantial number of voters used the plurality heuristic in the real elections, they did so sincerely, not strategically. Moreover, even though Thurstonian models do not force such agreement, the results show, in contrast to common wisdom about social choice rules, that the sincere social orders by Condorcet, Borda, plurality, and approval voting are identical in all 7 elections and in the Internet experiment. PsycINFO Database Record (c) 2007 APA, all rights reserved.

  14. Systemic administration of high-molecular weight hyaluronan stimulates wound healing in genetically diabetic mice.

    Science.gov (United States)

    Galeano, Mariarosaria; Polito, Francesca; Bitto, Alessandra; Irrera, Natasha; Campo, Giuseppe M; Avenoso, Angela; Calò, Margherita; Lo Cascio, Patrizia; Minutoli, Letteria; Barone, Mauro; Squadrito, Francesco; Altavilla, Domenica

    2011-07-01

    Hyaluronic acid (HA), an essential component of the extracellular matrix, is an efficient space filler that maintains hydration, serves as a substrate for assembly of proteoglycans and is involved in wound healing. Although numerous pieces of evidence demonstrate beneficial effects in promoting wound healing in diabetes, a systemic approach has never been tested. We used an incisional wound healing model in genetically diabetic mice to test the effects of systemic injection of HA. Diabetic (n=56) and normoglycemic (n=56) mice were subjected to incision and randomized (8 groups of 7 animals each) to receive HA at different doses, 7.5, 15 and 30mg/kg/i.p., or vehicle (0.9% NaCl solution) for 12days. At the end of the experiment animals were sacrificed and skin wounds were excised for histological, biochemical and molecular analysis. Histology revealed that the most effective dose to improve wound repair and angiogenesis in diabetic mice was 30mg/kg. Furthermore HA injection (30mg/kg) improved the altered healing pattern in diabetic animals, increased skin remodeling proteins TGF-β and transglutaminase-II and restored the altered expression of cyclin B1/Cdc2 complex. Evaluation of skin from diabetic animals injected with HA revealed also an increase in HA content, suggesting that systemic injection may be able to restore the reduced intracellular HA pool of diabetic mice. Finally HA markedly improved skin mechanical properties. These promising results, if confirmed in a clinical setting, may improve the care and management of diabetic patients. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Development of a molecular method for testing the effectiveness of UV systems on-site.

    Science.gov (United States)

    Nizri, Limor; Vaizel-Ohayon, Dalit; Ben-Amram, Hila; Sharaby, Yehonatan; Halpern, Malka; Mamane, Hadas

    2017-12-15

    We established a molecular method for quantifying ultraviolet (UV) disinfection efficacy using total bacterial DNA in a water sample. To evaluate UV damage to the DNA, we developed the "DNA damage" factor, which is a novel cultivation-independent approach that reveals UV-exposure efficiency by applying a simple PCR amplification method. The study's goal was to prove the feasibility of this method for demonstrating the efficiency of UV systems in the field using flow-through UV reactors. In laboratory-based experiments using seeded bacteria, the DNA damage tests demonstrated a good correlation between PCR products and UV dose. In the field, natural groundwater sampled before and after being subjected to the full-scale UV reactors was filtered, and the DNA extracted from the filtrate was subjected to PCR amplification for a 900-bp fragment of the 16S rRNA gene with initial DNA concentrations of 0.1 and 1 ng/μL. In both cases, the UV dose predicted and explained a significant proportion of the variance in the log inactivation ratio and DNA damage factor. Log inactivation ratio was very low, as expected in groundwater due to low initial bacterial counts, whereas the DNA damage factor was within the range of values obtained in the laboratory-based experiments. Consequently, the DNA damage factor reflected the true performance of the full-scale UV system during operational water flow by using the indigenous bacterial array present in a water sample. By applying this method, we were able to predict with high confidence, the UV reactor inactivation potential. For method validation, laboratory and field iterations are required to create a practical field calibration curve that can be used to determine the expected efficiency of the full-scale UV system in the field under actual operation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Molecular components and functions of the endocannabinoid system in mouse prefrontal cortex.

    Directory of Open Access Journals (Sweden)

    Mathieu Lafourcade

    2007-08-01

    Full Text Available Cannabinoids have deleterious effects on prefrontal cortex (PFC-mediated functions and multiple evidences link the endogenous cannabinoid (endocannabinoid system, cannabis use and schizophrenia, a disease in which PFC functions are altered. Nonetheless, the molecular composition and the physiological functions of the endocannabinoid system in the PFC are unknown.Here, using electron microscopy we found that key proteins involved in endocannabinoid signaling are expressed in layers v/vi of the mouse prelimbic area of the PFC: presynaptic cannabinoid CB1 receptors (CB1R faced postsynaptic mGluR5 while diacylglycerol lipase alpha (DGL-alpha, the enzyme generating the endocannabinoid 2-arachidonoyl-glycerol (2-AG was expressed in the same dendritic processes as mGluR5. Activation of presynaptic CB1R strongly inhibited evoked excitatory post-synaptic currents. Prolonged synaptic stimulation at 10Hz induced a profound long-term depression (LTD of layers V/VI excitatory inputs. The endocannabinoid -LTD was presynaptically expressed and depended on the activation of postsynaptic mGluR5, phospholipase C and a rise in postsynaptic Ca(2+ as predicted from the localization of the different components of the endocannabinoid system. Blocking the degradation of 2-AG (with URB 602 but not of anandamide (with URB 597 converted subthreshold tetanus to LTD-inducing ones. Moreover, inhibiting the synthesis of 2-AG with Tetrahydrolipstatin, blocked endocannabinoid-mediated LTD. All together, our data show that 2-AG mediates LTD at these synapses.Our data show that the endocannabinoid -retrograde signaling plays a prominent role in long-term synaptic plasticity at the excitatory synapses of the PFC. Alterations of endocannabinoid -mediated synaptic plasticity may participate to the etiology of PFC-related pathologies.

  17. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    Science.gov (United States)

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  18. Molecular collision theory

    CERN Document Server

    Child, M S

    2010-01-01

    This high-level monograph offers an excellent introduction to the theory required for interpretation of an increasingly sophisticated range of molecular scattering experiments. There are five helpful appendixes dealing with continuum wavefunctions, Green's functions, semi-classical connection formulae, curve-crossing in the momentum representation, and elements of classical mechanics.The contents of this volume have been chosen to emphasize the quantum mechanical and semi-classical nature of collision events, with little attention given to purely classical behavior. The treatment is essentiall

  19. On the quantification of the dissolved hydroxyl radicals in the plasma-liquid system using the molecular probe method

    Science.gov (United States)

    Ma, Yupengxue; Gong, Xinning; He, Bangbang; Li, Xiaofei; Cao, Dianyu; Li, Junshuai; Xiong, Qing; Chen, Qiang; Chen, Bing Hui; Huo Liu, Qing

    2018-04-01

    Hydroxyl (OH) radical is one of the most important reactive species produced by plasma-liquid interactions, and the OH in liquid phase (dissolved OH radical, OHdis) takes effect in many plasma-based applications due to its high reactivity. Therefore, the quantification of the OHdis in a plasma-liquid system is of great importance, and a molecular probe method usually used for the OHdis detection might be applied. Herein, we investigate the validity of using the molecular probe method to estimate the [OHdis] in the plasma-liquid system. Dimethyl sulfoxide is used as the molecular probe to estimate the [OHdis] in an air plasma-liquid system, and usually the estimation of [OHdis] is deduced by quantifying the OHdis-induced derivative, the formaldehyde (HCHO). The analysis indicates that the true concentration of the OHdis should be estimated from the sum of three terms: the formed HCHO, the existing OH scavengers, and the H2O2 formed from the OHdis. The results show that the measured [HCHO] needs to be corrected since the HCHO consumption is not negligible in the plasma-liquid system. We conclude from the results and the analysis that the molecular probe method generally underestimates the [OHdis] in the plasma-liquid system. If one wants to obtain the true concentration of the OHdis in the plasma-liquid system, one needs to know the consumption behavior of the OHdis-induced derivatives, the information of the OH scavengers (such as hydrated electron, atomic hydrogen besides the molecular probe), and also the knowledge of the H2O2 formed from the OHdis.

  20. The Wiphala Genomics: the deployment of molecular markers in small-scale potato crop systems in the Bolivian Andes

    NARCIS (Netherlands)

    Puente, D.

    2008-01-01

    The deployment of molecular markers in the small-scale potato systems in the Bolivian Andes takes place within two contradictory understandings of potato biodiversity. On the one hand, biodiversity is understood as raw material; farmers' varieties have no intrinsic value, value is added by breeders

  1. Deregulation of the ubiquitin-proteasome system is the predominant molecular pathology in OPMD animal models and patients

    DEFF Research Database (Denmark)

    Anvar, Seyed Yahya; hoen, Peter Ac; Venema, Andrea

    2011-01-01

    molecular pathways that are consistently associated with OPMD, we performed an integrated high-throughput transcriptome study in affected muscles of OPMD animal models and patients. The ubiquitin-proteasome system (UPS) was found to be the most consistently and significantly OPMD-deregulated pathway across...

  2. Some simulation aspects, from molecular systems to stochastic geometries of pebble bed reactors

    International Nuclear Information System (INIS)

    Mazzolo, A.

    2009-06-01

    After a brief presentation of his teaching and supervising activities, the author gives an overview of his research activities: investigation of atoms under high intensity magnetic field (investigation of the electronic structure under these fields), studies of theoretical and numerical electrochemistry (simulation coupling molecular dynamics and quantum calculations, comprehensive simulations of molecular dynamics), and studies relating stochastic geometry and neutron science

  3. Energy transformation in molecular electronic systems. Progress report, December 1, 1981-November 30, 1982

    International Nuclear Information System (INIS)

    Kasha, M.

    1982-01-01

    Summaries are presented of studies on: molecular translational-rotovibronic Hamiltonians for nonlinear and linear molecules, singlet oxygen in potassium superoxide-water, proton-transfer spectroscopy of water in chromones, mechanism of 4-level molecular lasers, and cationic/anionic potential in proton-transfer spectroscopy

  4. A hardware investigation of robotic SPECT for functional and molecular imaging onboard radiation therapy systems

    International Nuclear Information System (INIS)

    Yan, Susu; Tough, MengHeng; Bowsher, James; Yin, Fang-Fang; Cheng, Lin

    2014-01-01

    Purpose: To construct a robotic SPECT system and to demonstrate its capability to image a thorax phantom on a radiation therapy flat-top couch, as a step toward onboard functional and molecular imaging in radiation therapy. Methods: A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150 L110 robot). An imaging study was performed with a phantom (PET CT Phantom TM ), which includes five spheres of 10, 13, 17, 22, and 28 mm diameters. The phantom was placed on a flat-top couch. SPECT projections were acquired either with a parallel-hole collimator or a single-pinhole collimator, both without background in the phantom and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180° and 228°, respectively. The pinhole detector viewed an off-centered spherical common volume which encompassed the 28 and 22 mm spheres. The common volume for parallel-hole system was centered at the phantom which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the phantom and flat-top table while avoiding collision and maintaining the closest possible proximity to the common volume. The robot base and tool coordinates were used for image reconstruction. Results: The robotic SPECT system was able to maneuver parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector radius of rotation. Without background, all five spheres were visible in the reconstructed parallel-hole image, while four spheres, all except the smallest one, were visible in the reconstructed pinhole image. With background, three spheres of 17, 22, and 28 mm diameters were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameters) were readily observed in the pinhole

  5. On the abundance and general nature of the liquid-liquid phase transition in molecular systems

    International Nuclear Information System (INIS)

    Kurita, Rei; Tanaka, Hajime

    2005-01-01

    Even a single-component liquid may have more than two kinds of isotropic liquid states. The transition between these different states is called a liquid-liquid transition (LLT). An LLT has been considered to be a rather rare phenomenon, in particular for molecular liquids. Very recently, however, we found an LLT in triphenyl phosphite, which may be the first experimental observation of an LLT for molecular liquids. Here we report convincing evidence of the second example of LLT for another molecular liquid, n-butanol. Despite large differences in the chemical structure and the molecular shape between triphenyl phosphite and n-butanol, the basic features of the transformation kinetics are strikingly similar. This suggests that an LLT may not be a rare phenomenon restricted to specific liquids, but may exist in various molecular liquids, which have a tendency to form long-lived locally favoured structures due to anisotropic interactions (e.g., hydrogen bonding). (letter to the editor)

  6. Studies of the energy density functional and its derivatives in atomic and molecular systems

    International Nuclear Information System (INIS)

    Robles, J.

    1986-01-01

    The first chapter is a review of formal density functional theory, (DFT). In the second chapter, approximations to exact DFT are reviewed. In chapter three, the author proposes a modified molecular Thomas-Fermi, (TF) theory. He proceeds by imposing a continuity condition on the density. This avoids the singularities at the nuclei of classical TF. The method is sanctioned by Teller and Balasz theorems. However, it is found that while the classical TF theory is improved, the present method still predicts no-binding. In chapter four, it is suggested that the correlation energy, (E/sub c/), is proportional to the exchange energy, (K), E/sub c/ = cK. This idea is tested with Hartree-Fock (HF) and DFT data. In HF, c = 1/40 for atoms and c = 1/25 for molecules. Furthermore, the method is used to estimate dissociation energies. Thereafter, the author studies the chemical potential, (μ), of atoms (chapter five) and molecules (chapter six). In chapter seven, the concept of local pressure in an inhomogeneous electronic system is studied and extended, within the local thermodynamic formulation of DFT. Finally, appendix A provides the required mathematical framework (basic functional calculus) to understand this work, while appendix B is essentially a summary of the HF method

  7. Molecular insights into the origin of the Hox-TALE patterning system.

    Science.gov (United States)

    Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

    2014-03-18

    Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior-posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox-TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001.

  8. Soliton analysis in complex molecular systems: A zig-zag chain

    International Nuclear Information System (INIS)

    Christiansen, P.L.; Savin, A.V.; Zolotaryuk, A.V.

    1997-01-01

    A simple numerical method for seeking solitary wave solutions of a permanent profile in molecular systems of big complexity is presented. The method is essentially based on the minimization of a finite-dimensional function which is chosen under an appropriate discretization of time derivatives in equations of motion. In the present paper, it is applied to a zig-zag chain backbone of coupled particles, each of which has two degrees of freedom (longitudinal and transverse). Both topological and nontopological soliton solutions are treated for this chain when it is (i) subjected to a two-dimensional periodic substrate potential or (ii) considered as an isolated object, respectively. In the first case, which may be considered as a zig-zag generalization of the Frenkel-Kontorova chain model, two types of kink solutions with different topological charges, describing vacancies of one or two atoms (I- or II-kinks) and defects with excess one or two atoms in the chain (I- or II-antikinks), have been found. The second case (isolated chain) is a generalization of the well-known Fermi-Pasta-Ulam chain model, which takes into account transverse degrees of freedom of the chain molecules. Two types of stable nontopological soliton solutions which describe either (i) a supersonic solitary wave of longitudinal stretching accompanied by transverse slandering or supersonic pulses of longitudinal compression propagating together with localized transverse thickening (bulge) have been obtained. 32 refs., 11 figs

  9. Soliton Analysis in Complex Molecular Systems: A Zig-Zag Chain

    Science.gov (United States)

    Christiansen, P. L.; Savin, A. V.; Zolotaryuk, A. V.

    1997-06-01

    A simple numerical method for seeking solitary wavesolutions of a permanent profile in molecular systems of big complexity is presented. The method is essentially based on the minimization of a finite-dimensional function which is chosen under an appropriate discretization of time derivatives in equations of motion. In the present paper, it is applied to a zig-zag chain backbone of coupled particles, each of which has twodegrees of freedom (longitudinal and transverse). Both topological and nontopological soliton solutions are treated for this chain when it is (i) subjected to a two-dimensional periodic substrate potential or (ii) considered as an isolated object, respectively. In the first case, which may be considered as a zig-zag generalization of the Frenkel-Kontorova chain model, two types of kink solutions with different topological charges, describing vacancies of one or two atoms (I- or II-kinks) and defects with excess one or two atoms in the chain (I- or II-antikinks), have been found. The second case (isolated chain) is a generalization of the well-known Fermi-Pasta-Ulam chain model, which takes into account transverse degrees of freedom of the chain molecules. Two types of stable nontopological soliton solutions which describe either (i) a supersonic solitary wave of longitudinal stretching accompanied by transverse slendering or (ii) supersonic pulses of longitudinal compression propagating together with localized transverse thickening (bulge) have been obtained.

  10. Molecular characterization of circulating plasma cells in patients with active systemic lupus erythematosus.

    Directory of Open Access Journals (Sweden)

    Patricia L Lugar

    Full Text Available Systemic lupus erythematosus (SLE is a generalized autoimmune disease characterized by abnormal B cell activation and the occurrence of increased frequencies of circulating plasma cells (PC. The molecular characteristics and nature of circulating PC and B cells in SLE have not been completely characterized. Microarray analysis of gene expression was used to characterize circulating PC in subjects with active SLE. Flow cytometry was used to sort PC and comparator B cell populations from active SLE blood, normal blood and normal tonsil. The gene expression profiles of the sorted B cell populations were then compared. SLE PC exhibited a similar gene expression signature as tonsil PC. The differences in gene expression between SLE PC and normal tonsil PC and tonsil plasmablasts (PB suggest a mature Ig secreting cell phenotype in the former population. Despite this, SLE PC differed in expression of about half the genes from previously published gene expression profiles of normal bone marrow PC, indicating that these cells had not achieved a fully mature status. Abnormal expression of several genes, including CXCR4 and S1P(1, suggests a mechanism for the persistence of SLE PC in the circulation. All SLE B cell populations revealed an interferon (IFN gene signature previously only reported in unseparated SLE peripheral blood mononuclear cells. These data indicate that SLE PC are a unique population of Ig secreting cells with a gene expression profile indicative of a mature, but not fully differentiated phenotype.

  11. Source-sink interaction: a century old concept under the light of modern molecular systems biology.

    Science.gov (United States)

    Chang, Tian-Gen; Zhu, Xin-Guang; Raines, Christine

    2017-07-20

    Many approaches to engineer source strength have been proposed to enhance crop yield potential. However, a well-co-ordinated source-sink relationship is required finally to realize the promised increase in crop yield potential in the farmer's field. Source-sink interaction has been intensively studied for decades, and a vast amount of knowledge about the interaction in different crops and under different environments has been accumulated. In this review, we first introduce the basic concepts of source, sink and their interactions, then summarize current understanding of how source and sink can be manipulated through both environmental control and genetic manipulations. We show that the source-sink interaction underlies the diverse responses of crops to the same perturbations and argue that development of a molecular systems model of source-sink interaction is required towards a rational manipulation of the source-sink relationship for increased yield. We finally discuss both bottom-up and top-down routes to develop such a model and emphasize that a community effort is needed for development of this model. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  12. Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems

    Directory of Open Access Journals (Sweden)

    Josh Fass

    2018-04-01

    Full Text Available While Langevin integrators are popular in the study of equilibrium properties of complex systems, it is challenging to estimate the timestep-induced discretization error: the degree to which the sampled phase-space or configuration-space probability density departs from the desired target density due to the use of a finite integration timestep. Sivak et al., introduced a convenient approach to approximating a natural measure of error between the sampled density and the target equilibrium density, the Kullback-Leibler (KL divergence, in phase space, but did not specifically address the issue of configuration-space properties, which are much more commonly of interest in molecular simulations. Here, we introduce a variant of this near-equilibrium estimator capable of measuring the error in the configuration-space marginal density, validating it against a complex but exact nested Monte Carlo estimator to show that it reproduces the KL divergence with high fidelity. To illustrate its utility, we employ this new near-equilibrium estimator to assess a claim that a recently proposed Langevin integrator introduces extremely small configuration-space density errors up to the stability limit at no extra computational expense. Finally, we show how this approach to quantifying sampling bias can be applied to a wide variety of stochastic integrators by following a straightforward procedure to compute the appropriate shadow work, and describe how it can be extended to quantify the error in arbitrary marginal or conditional distributions of interest.

  13. A Snapshot of Serial Rape: An Investigation of Criminal Sophistication and Use of Force on Victim Injury and Severity of the Assault.

    Science.gov (United States)

    de Heer, Brooke

    2016-02-01

    Prior research on rapes reported to law enforcement has identified criminal sophistication and the use of force against the victim as possible unique identifiers to serial rape versus one-time rape. This study sought to contribute to the current literature on reported serial rape by investigating how the level of criminal sophistication of the rapist and use of force used were associated with two important outcomes of rape: victim injury and overall severity of the assault. In addition, it was evaluated whether rapist and victim ethnicity affected these relationships. A nation-wide sample of serial rape cases reported to law enforcement collected by the Federal Bureau of Investigation (FBI) was analyzed (108 rapists, 543 victims). Results indicated that serial rapists typically used a limited amount of force against the victim and displayed a high degree of criminal sophistication. In addition, the more criminally sophisticated the perpetrator was, the more sexual acts he performed on his victim. Finally, rapes between a White rapist and White victim were found to exhibit higher levels of criminal sophistication and were more severe in terms of number and types of sexual acts committed. These findings provide a more in-depth understanding of serial rape that can inform both academics and practitioners in the field about contributors to victim injury and severity of the assault. © The Author(s) 2014.

  14. A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

    Science.gov (United States)

    Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

    2015-02-01

    The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

  15. Broadening the functionality of a J-protein/Hsp70 molecular chaperone system.

    Science.gov (United States)

    Schilke, Brenda A; Ciesielski, Szymon J; Ziegelhoffer, Thomas; Kamiya, Erina; Tonelli, Marco; Lee, Woonghee; Cornilescu, Gabriel; Hines, Justin K; Markley, John L; Craig, Elizabeth A

    2017-10-01

    By binding to a multitude of polypeptide substrates, Hsp70-based molecular chaperone systems perform a range of cellular functions. All J-protein co-chaperones play the essential role, via action of their J-domains, of stimulating the ATPase activity of Hsp70, thereby stabilizing its interaction with substrate. In addition, J-proteins drive the functional diversity of Hsp70 chaperone systems through action of regions outside their J-domains. Targeting to specific locations within a cellular compartment and binding of specific substrates for delivery to Hsp70 have been identified as modes of J-protein specialization. To better understand J-protein specialization, we concentrated on Saccharomyces cerevisiae SIS1, which encodes an essential J-protein of the cytosol/nucleus. We selected suppressors that allowed cells lacking SIS1 to form colonies. Substitutions changing single residues in Ydj1, a J-protein, which, like Sis1, partners with Hsp70 Ssa1, were isolated. These gain-of-function substitutions were located at the end of the J-domain, suggesting that suppression was connected to interaction with its partner Hsp70, rather than substrate binding or subcellular localization. Reasoning that, if YDJ1 suppressors affect Ssa1 function, substitutions in Hsp70 itself might also be able to overcome the cellular requirement for Sis1, we carried out a selection for SSA1 suppressor mutations. Suppressing substitutions were isolated that altered sites in Ssa1 affecting the cycle of substrate interaction. Together, our results point to a third, additional means by which J-proteins can drive Hsp70's ability to function in a wide range of cellular processes-modulating the Hsp70-substrate interaction cycle.

  16. Molecular imaging of in vivo redox dynamics using magnetic resonance system

    International Nuclear Information System (INIS)

    Utsumi, Hideo; Yasukawa, Keiji

    2008-01-01

    Homeostatic failure through redox systems in vivo results in abnormality in mitochondrial function, protein expression and metabolism leading to many diseases like lifestyle related ones and cancer. It is therefore important to see redox dynamics for early prevention of the diseases. This paper describes development of machines for electron spin resonance (ESR) imaging of the redox state, for Overhauser Effect MRI (OMRI), application of nitroxyl-probes and state of redox project by authors. They have developed the ESR equipments hitherto, including the latest 300 MHz one, with which images of a mouse given carbamoyl-PROXYL probe are obtained and fused with MRI images for anatomical positioning: resonator for both ESR and MRI coils has been developed for animal images. Philips OMRI machine has been able to give separate images of reduction and oxidation in animals given appropriate probe compounds, which lead to molecular imaging of redox using such probes as 14 N- and 15 N-nitroxyl radicals with different membrane permeability. Application of nitroxyl-radicals like hydroxyl-TEMPO has made it possible for the animal diseases caused by oxidative stress to be analyzed by ESR/spin probe method, and derivatization of the probe results in detection of its distribution in various cell and body areas even in nanometer-space. Authors' project concerns the development of the processing system of redox dynamics/OMRI-integrated images, of better probe complexes and application of these to actual model animals. The techniques are thought to be important in the fields of medicare and new drug development in future. (R.T.)

  17. A molecular identification system for grasses: a novel technology for forensic botany.

    Science.gov (United States)

    Ward, J; Peakall, R; Gilmore, S R; Robertson, J

    2005-09-10

    Our present inability to rapidly, accurately and cost-effectively identify trace botanical evidence remains the major impediment to the routine application of forensic botany. Grasses are amongst the most likely plant species encountered as forensic trace evidence and have the potential to provide links between crime scenes and individuals or other vital crime scene information. We are designing a molecular DNA-based identification system for grasses consisting of several PCR assays that, like a traditional morphological taxonomic key, provide criteria that progressively identify an unknown grass sample to a given taxonomic rank. In a prior study of DNA sequences across 20 phylogenetically representative grass species, we identified a series of potentially informative indels in the grass mitochondrial genome. In this study we designed and tested five PCR assays spanning these indels and assessed the feasibility of these assays to aid identification of unknown grass samples. We confirmed that for our control set of 20 samples, on which the design of the PCR assays was based, the five primer combinations produced the expected results. Using these PCR assays in a 'blind test', we were able to identify 25 unknown grass samples with some restrictions. Species belonging to genera represented in our control set were all correctly identified to genus with one exception. Similarly, genera belonging to tribes in the control set were correctly identified to the tribal level. Finally, for those samples for which neither the tribal or genus specific PCR assays were designed, we could confidently exclude these samples from belonging to certain tribes and genera. The results confirmed the utility of the PCR assays and the feasibility of developing a robust full-scale usable grass identification system for forensic purposes.

  18. The characterization of an economic and portable LED-based photoacoustic imaging system to facilitate molecular imaging.

    Science.gov (United States)

    Hariri, Ali; Lemaster, Jeanne; Wang, Junxin; Jeevarathinam, AnanthaKrishnan S; Chao, Daniel L; Jokerst, Jesse V

    2018-03-01

    Photoacoustic imaging (PAI) is a non-invasive, high-resolution hybrid imaging modality that combines optical excitation and ultrasound detection. PAI can image endogenous chromophores (melanin, hemoglobin, etc.) and exogenous contrast agents in different medical applications. However, most current equipment uses sophisticated and complicated OPO lasers with tuning and stability features inconsistent with broad clinical deployment. As the number of applications of PAI in medicine increases, there is an urgent need to make the imaging equipment more compact, portable, and affordable. Here, portable light emitting diode - based photoacoustic imaging (PLED-PAI) was introduced and characterized in terms of system specifications, light source characterizations, photoacoustic spatial/temporal resolution, and penetration. The system uses two LED arrays attached to the sides of a conventional ultrasound transducer. The LED pulse repetition rate is tunable between 1 K Hz, 2 K Hz, 3 K Hz, and 4 K Hz. The axial resolution was 0.268 mm, and the lateral resolution was between 0.55 and 0.59 mm. The system could detect optical absorber (pencil lead) at a depth of 3.2 cm and the detection limits of indocyanine green (ICG) and methylene blue (MB) were 9 μM and 0.78 mM. In vivo imaging of labeled human mesenchymal stem cells was achieved to confirm compatibility with small animal imaging. The characterization we report here may have value to other groups evaluating commercially available photoacoustic imaging equipment.

  19. Preparation of Low Molecular Weight Gelatin Using Microwave Discharge Electrodeless Lamp/TiO2 Photocatalyst Hybrid System.

    Science.gov (United States)

    Lee, Do-Jin; Kim, Hangun; Park, Young-Kwon; Kim, Byung Hoon; Lee, Heon; Jungf, Sana-Chul

    2016-02-01

    In this study, an MDEL/TiO2 photocatalyst hybrid system was applied to the production of low molecular weight gelatin. The molecular weight of produed gelatin decreased with increasing microwave intensity and increasing treatment time. The abscission of the chemical bonds between the con- stituents of gelatin by photocatalytic reaction did not alter the characteristics of gelatin. Formation of any by-products due to side reaction was not observed. It is suggested that gelatin was depolymerized by hydroxyl radicals produced during the MDEL/TiO2 photochemical reaction.

  20. Deregulation of the ubiquitin-proteasome system is the predominant molecular pathology in OPMD animal models and patients

    DEFF Research Database (Denmark)

    Anvar, Seyed Yahya; hoen, Peter Ac; Venema, Andrea

    2011-01-01

    Oculopharyngeal muscular dystrophy (OPMD) is a late-onset progressive muscle disorder caused by a poly-alanine expansion mutation in the Poly(A) Binding Protein Nuclear 1 (PABPN1). The molecular mechanisms that regulate disease onset and progression are largely unknown. In order to identify...... molecular pathways that are consistently associated with OPMD, we performed an integrated high-throughput transcriptome study in affected muscles of OPMD animal models and patients. The ubiquitin-proteasome system (UPS) was found to be the most consistently and significantly OPMD-deregulated pathway across...

  1. Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

    Science.gov (United States)

    Nistor, Razvan A.

    The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high

  2. Background field removal technique using regularization enabled sophisticated harmonic artifact reduction for phase data with varying kernel sizes.

    Science.gov (United States)

    Kan, Hirohito; Kasai, Harumasa; Arai, Nobuyuki; Kunitomo, Hiroshi; Hirose, Yasujiro; Shibamoto, Yuta

    2016-09-01

    An effective background field removal technique is desired for more accurate quantitative susceptibility mapping (QSM) prior to dipole inversion. The aim of this study was to evaluate the accuracy of regularization enabled sophisticated harmonic artifact reduction for phase data with varying spherical kernel sizes (REV-SHARP) method using a three-dimensional head phantom and human brain data. The proposed REV-SHARP method used the spherical mean value operation and Tikhonov regularization in the deconvolution process, with varying 2-14mm kernel sizes. The kernel sizes were gradually reduced, similar to the SHARP with varying spherical kernel (VSHARP) method. We determined the relative errors and relationships between the true local field and estimated local field in REV-SHARP, VSHARP, projection onto dipole fields (PDF), and regularization enabled SHARP (RESHARP). Human experiment was also conducted using REV-SHARP, VSHARP, PDF, and RESHARP. The relative errors in the numerical phantom study were 0.386, 0.448, 0.838, and 0.452 for REV-SHARP, VSHARP, PDF, and RESHARP. REV-SHARP result exhibited the highest correlation between the true local field and estimated local field. The linear regression slopes were 1.005, 1.124, 0.988, and 0.536 for REV-SHARP, VSHARP, PDF, and RESHARP in regions of interest on the three-dimensional head phantom. In human experiments, no obvious errors due to artifacts were present in REV-SHARP. The proposed REV-SHARP is a new method combined with variable spherical kernel size and Tikhonov regularization. This technique might make it possible to be more accurate backgroud field removal and help to achive better accuracy of QSM. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. An integrated approach of network-based systems biology, molecular docking, and molecular dynamics approach to unravel the role of existing antiviral molecules against AIDS-associated cancer.

    Science.gov (United States)

    Omer, Ankur; Singh, Poonam

    2017-05-01

    A serious challenge in cancer treatment is to reposition the activity of various already known drug candidates against cancer. There is a need to rewrite and systematically analyze the detailed mechanistic aspect of cellular networks to gain insight into the novel role played by various molecules. Most Human Immunodeficiency Virus infection-associated cancers are caused by oncogenic viruses like Human Papilloma Viruses and Epstein-Bar Virus. As the onset of AIDS-associated cancers marks the severity of AIDS, there might be possible interconnections between the targets and mechanism of both the diseases. We have explored the possibility of certain antiviral compounds to act against major AIDS-associated cancers: Kaposi's Sarcoma, Non-Hodgkin Lymphoma, and Cervical Cancer with the help of systems pharmacology approach that includes screening for targets and molecules through the construction of a series of drug-target and drug-target-diseases network. Two molecules (Calanolide A and Chaetochromin B) and the target "HRAS" were finally screened with the help of molecular docking and molecular dynamics simulation. The results provide novel antiviral molecules against HRAS target to treat AIDS defining cancers and an insight for understanding the pharmacological, therapeutic aspects of similar unexplored molecules against various cancers.

  4. Lanthanides in molecular magnetism: old tools in a new field.

    Science.gov (United States)

    Sorace, Lorenzo; Benelli, Cristiano; Gatteschi, Dante

    2011-06-01

    In this tutorial review we discuss some basic aspects concerning the magnetic properties of rare-earth ions, which are currently the subject of a renovated interest in the field of molecular magnetism, after the discovery that slow relaxation of the magnetization at liquid nitrogen temperature can occur in mononuclear complexes of these ions. Focusing on Dy(III) derivatives a tutorial discussion is given of the relation of the crystal field parameters, which determine the anisotropy of these systems and consequently their interesting magnetic properties, with the geometry of the coordination sphere around the lanthanide centre and with the pattern of f orbitals. The problem of systems of low point symmetry is also addressed by showing how detailed single crystal investigation, coupled to more sophisticated calculation procedures, is an absolute necessity to obtain meaningful structure-property relationships in these systems.

  5. Studies of the charge instabilities in the complex nano-objects: clusters and bio-molecular systems

    International Nuclear Information System (INIS)

    Manil, B.

    2007-11-01

    For the last 6 years, my main research works focused on i) the Coulomb instabilities and the fragmentation processes of fullerenes and clusters of fullerenes ii) the stability and the reactivity of complex bio-molecular systems. Concerning the clusters of fullerenes, which are van der Waals type clusters, we have shown that the multiply charged species, obtained in collisions with slow highly charged ions, keep their structural properties but become very good electric conductor. In another hand, with the aim to understand the role of the biologic environment at the molecular scale in the irradiation damage of complex biomolecules, we have studied the charge stabilities of clusters of small biomolecules and the dissociation processes of larger nano-hydrated biomolecules. Theses studies have shown that first, specific molecular recognition mechanisms continue to exist in gas phase and secondly, a small and very simple biochemical environment is enough to change the dynamics of instabilities. (author)

  6. Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

    Science.gov (United States)

    Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

    2015-12-01

    Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

  7. Building New Bridges between In Vitro and In Vivo in Early Drug Discovery: Where Molecular Modeling Meets Systems Biology.

    Science.gov (United States)

    Pearlstein, Robert A; McKay, Daniel J J; Hornak, Viktor; Dickson, Callum; Golosov, Andrei; Harrison, Tyler; Velez-Vega, Camilo; Duca, José

    2017-01-01

    Cellular drug targets exist within networked function-generating systems whose constituent molecular species undergo dynamic interdependent non-equilibrium state transitions in response to specific perturbations (i.e.. inputs). Cellular phenotypic behaviors are manifested through the integrated behaviors of such networks. However, in vitro data are frequently measured and/or interpreted with empirical equilibrium or steady state models (e.g. Hill, Michaelis-Menten, Briggs-Haldane) relevant to isolated target populations. We propose that cells act as analog computers, "solving" sets of coupled "molecular differential equations" (i.e. represented by populations of interacting species)via "integration" of the dynamic state probability distributions among those populations. Disconnects between biochemical and functional/phenotypic assays (cellular/in vivo) may arise with targetcontaining systems that operate far from equilibrium, and/or when coupled contributions (including target-cognate partner binding and drug pharmacokinetics) are neglected in the analysis of biochemical results. The transformation of drug discovery from a trial-and-error endeavor to one based on reliable design criteria depends on improved understanding of the dynamic mechanisms powering cellular function/dysfunction at the systems level. Here, we address the general mechanisms of molecular and cellular function and pharmacological modulation thereof. We outline a first principles theory on the mechanisms by which free energy is stored and transduced into biological function, and by which biological function is modulated by drug-target binding. We propose that cellular function depends on dynamic counter-balanced molecular systems necessitated by the exponential behavior of molecular state transitions under non-equilibrium conditions, including positive versus negative mass action kinetics and solute-induced perturbations to the hydrogen bonds of solvating water versus kT. Copyright© Bentham

  8. Associations between the molecular and optical properties of dissolved organic matter in the Florida Everglades, a model coastal wetland system

    Science.gov (United States)

    Wagner, Sasha; Jaffe, Rudolf; Cawley, Kaelin; Dittmar, Thorsten; Stubbins, Aron

    2015-11-01

    Optical properties are easy-to-measure proxies for dissolved organic matter (DOM) composition, source and reactivity. However, the molecular signature of DOM associated with such optical parameters remains poorly defined. The Florida coastal Everglades is a subtropical wetland with diverse vegetation (e.g., sawgrass prairies, mangrove forests, seagrass meadows) and DOM sources (e.g., terrestrial, microbial and marine). As such, the Everglades is an excellent model system from which to draw samples of diverse origin and composition to allow classically-defined optical properties to be linked to molecular properties of the DOM pool. We characterized a suite of seasonally- and spatially-collected DOM samples using optical measurements (EEM-PARAFAC, SUVA254, S275-295, S350-400, SR, FI, freshness index and HIX) and ultrahigh resolution mass spectrometry (FTICR-MS). Spearman’s rank correlations between FTICR-MS signal intensities of individual molecular formulae and optical properties determined which molecular formulae were associated with each PARAFAC component and optical index. The molecular families that tracked with the optical indices were generally in agreement with conventional biogeochemical interpretations. Therefore, although they represent only a small portion of the bulk DOM pool, absorbance and fluorescence measurements appear to be appropriate proxies for the aquatic cycling of both optically-active and associated optically-inactive DOM in coastal wetlands.

  9. Associations between the molecular and optical properties of dissolved organic matter in the Florida Everglades, a model coastal wetland system

    Directory of Open Access Journals (Sweden)

    Sasha eWagner

    2015-11-01

    Full Text Available Optical properties are easy-to-measure proxies for dissolved organic matter (DOM composition, source and reactivity. However, the molecular signature of DOM associated with such optical parameters remains poorly defined. The Florida coastal Everglades is a subtropical wetland with diverse vegetation (e.g., sawgrass prairies, mangrove forests, seagrass meadows and DOM sources (e.g., terrestrial, microbial and marine. As such, the Everglades is an excellent model system from which to draw samples of diverse origin and composition to allow classically-defined optical properties to be linked to molecular properties of the DOM pool. We characterized a suite of seasonally- and spatially-collected DOM samples using optical measurements (EEM-PARAFAC, SUVA254, S275-295, S350-400, SR, FI, freshness index and HIX and ultrahigh resolution mass spectrometry (FTICR-MS. Spearman’s rank correlations between FTICR-MS signal intensities of individual molecular formulae and optical properties determined which molecular formulae were associated with each PARAFAC component and optical index. The molecular families that tracked with the optical indices were generally in agreement with conventional biogeochemical interpretations. Therefore, although they represent only a small portion of the bulk DOM pool, absorbance and fluorescence measurements appear to be appropriate proxies for the aquatic cycling of both optically-active and associated optically-inactive DOM in coastal wetlands.

  10. Molecular current switch: principles and photoelectronic characterization of the model system

    Czech Academy of Sciences Publication Activity Database

    Vala, M.; Weiter, M.; Nešpůrek, Stanislav

    2005-01-01

    Roč. 15, č. 3 (2005), s. 28 ISSN 1210-7409 Institutional research plan: CEZ:AV0Z40500505 Keywords : molecular electronics * photochromism * charge transport Subject RIV: CD - Macromolecular Chemistry

  11. On the basis of molecular orbitals for relativistic bound systems of many bodies

    International Nuclear Information System (INIS)

    Cook, A.H.

    1987-09-01

    The quasi-relativistic Hamiltonian for bound states of many bodies proposed in previous articles (Cook, 1986, 1987a) is shown to provide a basis for the molecular orbital scheme of constructing wavefunctions and calculating eigenenergies. (author). 5 refs

  12. Unique molecular landscapes in cancer: implications for individualized, curated drug combinations.

    Science.gov (United States)

    Wheler, Jennifer; Lee, J Jack; Kurzrock, Razelle

    2014-12-15

    With increasingly sophisticated technologies in molecular biology and "omic" platforms to analyze patients' tumors, more molecular diversity and complexity in cancer are being observed. Recently, we noted unique genomic profiles in a group of patients with metastatic breast cancer based on an analysis with next-generation sequencing. Among 57 consecutive patients, no two had the same molecular portfolio. Applied genomics therefore appears to represent a disruptive innovation in that it unveils a heterogeneity to metastatic cancer that may be ill-suited to canonical clinical trials and practice paradigms. Upon recognizing that patients have unique tumor landscapes, it is possible that there may be a "mismatch" between our traditional clinical trials system that selects patients based on common characteristics to evaluate a drug (drug-centric approach) and optimal treatment based on curated, individualized drug combinations for each patient (patient-centric approach). ©2014 American Association for Cancer Research.

  13. Update 0.2 to "pysimm: A python package for simulation of molecular systems"

    Science.gov (United States)

    Demidov, Alexander G.; Fortunato, Michael E.; Colina, Coray M.

    2018-01-01

    An update to the pysimm Python molecular simulation API is presented. A major part of the update is the implementation of a new interface with CASSANDRA - a modern, versatile Monte Carlo molecular simulation program. Several significant improvements in the LAMMPS communication module that allow better and more versatile simulation setup are reported as well. An example of an application implementing iterative CASSANDRA-LAMMPS interaction is illustrated.

  14. [Low-grade systemic inflammation and the development of metabolic diseases: from the molecular evidence to the clinical practice].

    Science.gov (United States)

    León-Pedroza, José Israel; González-Tapia, Luis Alonso; del Olmo-Gil, Esteban; Castellanos-Rodríguez, Diana; Escobedo, Galileo; González-Chávez, Antonio

    2015-01-01

    Systemic inflammation is characterised by high circulating levels of inflammatory cytokines and increased macrophage infiltration in peripheral tissues. Most importantly, this inflammatory state does not involve damage or loss of function of the infiltrated tissue, which is a distinctive feature of the low-grade systemic inflammation. The term "meta-inflammation" has also been used to refer to the low-grade systemic inflammation due to its strong relationship with the development of cardio-metabolic diseases in obesity. A review is presented on the recent clinical and experimental evidence concerning the role of adipose tissue inflammation as a key mediator of low-grade systemic inflammation. Furthermore, the main molecular mechanisms involved in the inflammatory polarization of macrophages with the ability to infiltrate both the adipose tissue and the vascular endothelium via activation of toll-like receptors by metabolic damage-associated molecular patterns, such as advanced glycation-end products and oxidized lipoproteins, is discussed. Finally, a review is made of the pathogenic mechanisms through which the low-grade systemic inflammation contributes to develop insulin resistance, dyslipidaemia, atherogenesis, type 2 diabetes, and hypertension in obese individuals. A better understanding of the molecular mechanisms of low-grade systemic inflammation in promoting cardio-metabolic diseases is necessary, in order to further design novel anti-inflammatory therapies that take into consideration clinical data, as well as the circulating levels of cytokines, immune cells, and metabolic damage-associated molecular patterns in each patient. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

  15. A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks

    Directory of Open Access Journals (Sweden)

    Xuezhong Zhou

    2018-05-01

    Full Text Available The International Classification of Diseases (ICD relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. Keywords: Disease taxonomy, Network medicine, Disease phenotypes, Molecular profiles, Precision medicine

  16. The Annotation, Mapping, Expression and Network (AMEN suite of tools for molecular systems biology

    Directory of Open Access Journals (Sweden)

    Primig Michael

    2008-02-01

    Full Text Available Abstract Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i uploading and pre-processing data from microarray expression profiling experiments, (ii detecting groups of significantly co-expressed genes, and (iii searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.

  17. Systems biological approach of molecular descriptors connectivity: optimal descriptors for oral bioavailability prediction.

    Science.gov (United States)

    Ahmed, Shiek S S J; Ramakrishnan, V

    2012-01-01

    Poor oral bioavailability is an important parameter accounting for the failure of the drug candidates. Approximately, 50% of developing drugs fail because of unfavorable oral bioavailability. In silico prediction of oral bioavailability (%F) based on physiochemical properties are highly needed. Although many computational models have been developed to predict oral bioavailability, their accuracy remains low with a significant number of false positives. In this study, we present an oral bioavailability model based on systems biological approach, using a machine learning algorithm coupled with an optimal discriminative set of physiochemical properties. The models were developed based on computationally derived 247 physicochemical descriptors from 2279 molecules, among which 969, 605 and 705 molecules were corresponds to oral bioavailability, intestinal absorption (HIA) and caco-2 permeability data set, respectively. The partial least squares discriminate analysis showed 49 descriptors of HIA and 50 descriptors of caco-2 are the major contributing descriptors in classifying into groups. Of these descriptors, 47 descriptors were commonly associated to HIA and caco-2, which suggests to play a vital role in classifying oral bioavailability. To determine the best machine learning algorithm, 21 classifiers were compared using a bioavailability data set of 969 molecules with 47 descriptors. Each molecule in the data set was represented by a set of 47 physiochemical properties with the functional relevance labeled as (+bioavailability/-bioavailability) to indicate good-bioavailability/poor-bioavailability molecules. The best-performing algorithm was the logistic algorithm. The correlation based feature selection (CFS) algorithm was implemented, which confirms that these 47 descriptors are the fundamental descriptors for oral bioavailability prediction. The logistic algorithm with 47 selected descriptors correctly predicted the oral bioavailability, with a predictive accuracy

  18. Molecular identification of the mode of interaction of nitrous oxide with the opiate receptor system

    Energy Technology Data Exchange (ETDEWEB)

    Wallar, D D

    1985-01-01

    The discovery of the opioid receptors in 1973 has led to a great deal of in vivo and in vitro research in order to understand the mechanism of binding of endogenous and synthetic opiate ligands. The use of nitrous oxide (N/sub 2/O) in anaesthesia is well documented. However, at lower concentrations N/sub 2/O produces analgesia. In 1976, it was reported that N/sub 2/O analgesia in man could be modified by the opiate antagonist naloxone. This clearly linked nitrous oxide analgesia to the opioid receptor system. It is the purpose of this dissertation to examine the molecular mechanism of action of N/sub 2/O at the opioid receptor through the use of in vitro binding studies. In addition, a model of the opioid receptor will be proposed. The following radiolabelled ligands were used in classical competitive binding assays to determine K (sub D),B(sub max), and IC/sub 50/ values in the presence of nitrous oxide and other control gases: dihydromorphine, N-allyl-N-normetazocine (SKF 10,047), and ethylketocyclazocine, for putative ..mu.., sigma and kappa opioid binding sites, respectively. All assays were performed using rat forebrain homogenates suspended in buffer previously saturated with the gas. Results indicate that N/sub 2/O differentially affects the binding kinetics of dihydromorphine. The binding kinetics of SKF 10,047 or ethylketocyclazocine were not altered significantly by N/sub 2/O indicating that N/sub 2/O is specific in its effects for the putative ..mu..-binding site. It is suggested that N/sub 2/O exerts its analgesic effects by perturbation of protein/lipid interactions within a multiple binding site opioid receptor complex.

  19. Study of the interaction of multiply charged ions and complex systems of biological interest: effects of the molecular environment

    International Nuclear Information System (INIS)

    Capron, Michael

    2011-01-01

    This PhD thesis describes the experimental study of the interaction between slow multiply charged ions (tens of keV) and molecular systems of biological interest (amino acids and nucleobases). It is the aim to identify and to better understand the effect of a molecular environment on different collision induced phenomena. To do so, the time of flight spectra of cationic products emerging from collisions with isolated molecules as well as clusters are compared. It is shown that the molecular environment protects the molecule as it allows to distribute the transferred energies and charges over the whole system (global decrease of the fragmentation and quenching of some fragmentation channels). Furthermore, in the case of adenine clusters, the molecular environment weakens some intramolecular bonds. Moreover, products of chemical reactions are observed concerning proton transfer processes in hydrated cluster of adenine and the formation of peptides bonds between beta-alanine molecules in a cluster. The latter finding is studied as a function of the cluster size and type of the projectile. Some criteria for peptide bond formation, such as flexibility and geometry of the molecule, are investigated for different amino acids. (author)

  20. Metal-Based Systems for Molecular Imaging Applications - COST D38 Annual Workshop - Scientific Program and Abstracts

    International Nuclear Information System (INIS)

    Mikolajczak, R.

    2009-01-01

    The main objective of the Action is the development of metal-based imaging probes for cellular and molecular imaging applications, based on MRI, PET, SPECT and optical imaging that will facilitate early diagnosis, assessment of disease progression and treatment evaluation.The goal of this Action is to further the development of innovative imaging probes through the pursuit of innovations in a number of different areas, ranging from the design of imaging units endowed with enhanced sensitivity to the control of the structural and electronic determinants responsible for the molecular recognition of the target molecule.At present, in vivo diagnostic systems basically assess the structure and function of human organs. Therefore, for important diseases such as cancer and cardiovascular pathologies,and also diseases of the central nervous system, only the late symptoms are detected. It is expected that the advances in genomics and proteomics will have a tremendous impact on human health care of the future. However, advances in molecular biology are already redefining diseases in terms of molecular abnormalities. With this knowledge, new generations of diagnostic imaging agents can be defined that aim at the detection of those molecular processes in vivo.The molecular imaging approach offers a great potential for earlier detection and characterisation of disease, and evaluation of treatment. However, more research is necessary to bring these ideas to clinical applications and a key aspect relates to the development of high-specificity, high-sensitivity imaging probes for the different detection modalities. Additionally, the Action includes research activities dealing with the exploitation of peculiar nuclear properties of given isotopes for therapeutic effects, thus integrating the diagnostic and the therapeutic stages.Apart from its use in early diagnosis in clinical practice, the molecular imaging approach will have also a major impact on the development of new

  1. Rational Design of Molecular Gelator - Solvent Systems Guided by Solubility Parameters

    Science.gov (United States)

    Lan, Yaqi

    Self-assembled architectures, such as molecular gels, have attracted wide interest among chemists, physicists and engineers during the past decade. However, the mechanism behind self-assembly remains largely unknown and no capability exists to predict a priori whether a small molecule will gelate a specific solvent or not. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (logP), to Henry's law constants (HLC), to solvatochromic ET(30) parameters, to Kamlet-Taft parameters (beta, alpha and pi), to Hansen solubility parameters (deltap, deltad, deltah), etc., are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries.

  2. Phthalocyanine-nanocarbon ensembles: from discrete molecular and supramolecular systems to hybrid nanomaterials.

    Science.gov (United States)

    Bottari, Giovanni; de la Torre, Gema; Torres, Tomas

    2015-04-21

    Phthalocyanines (Pcs) are macrocyclic and aromatic compounds that present unique electronic features such as high molar absorption coefficients, rich redox chemistry, and photoinduced energy/electron transfer abilities that can be modulated as a function of the electronic character of their counterparts in donor-acceptor (D-A) ensembles. In this context, carbon nanostructures such as fullerenes, carbon nanotubes (CNTs), and, more recently, graphene are among the most suitable Pc "companions". Pc-C60 ensembles have been for a long time the main actors in this field, due to the commercial availability of C60 and the well-established synthetic methods for its functionalization. As a result, many Pc-C60 architectures have been prepared, featuring different connectivities (covalent or supramolecular), intermolecular interactions (self-organized or molecularly dispersed species), and Pc HOMO/LUMO levels. All these elements provide a versatile toolbox for tuning the photophysical properties in terms of the type of process (photoinduced energy/electron transfer), the nature of the interactions between the electroactive units (through bond or space), and the kinetics of the formation/decay of the photogenerated species. Some recent trends in this field include the preparation of stimuli-responsive multicomponent systems with tunable photophysical properties and highly ordered nanoarchitectures and surface-supported systems showing high charge mobilities. A breakthrough in the Pc-nanocarbon field was the appearance of CNTs and graphene, which opened a new avenue for the preparation of intriguing photoresponsive hybrid ensembles showing light-stimulated charge separation. The scarce solubility of these 1-D and 2-D nanocarbons, together with their lower reactivity with respect to C60 stemming from their less strained sp(2) carbon networks, has not meant an unsurmountable limitation for the preparation of variety of Pc-based hybrids. These systems, which show improved

  3. The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

    International Nuclear Information System (INIS)

    Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plecháč, Petr

    2015-01-01

    Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems

  4. The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware 19716 (United States)

    2015-08-28

    Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.

  5. Sophisticated Epistemologies of Physics versus High-Stakes Tests: How Do Elite High School Students Respond to Competing Influences about How to Learn Physics?

    Science.gov (United States)

    Yerdelen-Damar, Sevda; Elby, Andrew

    2016-01-01

    This study investigates how elite Turkish high school physics students claim to approach learning physics when they are simultaneously (i) engaged in a curriculum that led to significant gains in their epistemological sophistication and (ii) subject to a high-stakes college entrance exam. Students reported taking surface (rote) approaches to…

  6. A tunable pH-sensing system based on Ag nanoclusters capped by hyperbranched polyethyleneimine with different molecular weights.

    Science.gov (United States)

    Qu, Fei; Zou, Xuan; Kong, Rongmei; You, Jinmao

    2016-01-01

    In this assay, a tunable pH sensing system was developed based on Ag nanoclusters (Ag NCs) capped by hyperbranched polyethyleneimine (PEI) with different molecular weights (abbreviated as Ag NC-PEIs). For instance, when the molecular weight of PEI was 600 or 1800, the fluorescence intensities of Ag NCs exhibited a linear fashion over the pH range 4.10-7.96; when the molecular weight of PEI was 25,000, the pH linear range was from 4.78 to 7.96; when the molecular weight of PEI was 70,000, the pH linear range was 6.09-8.95. According to the molecular weight of PEI 600/1800, 25,000, and 70,000, the color change point was pH 4.10-4.78, 5.33-6.09, and 6.09-6.80, respectively. Therefore, Ag NC-PEI 600 and 1800 were proper to acid conditions; Ag NC-PEI 25,000 was sensitive to weak acid media; while Ag NC-PEI 70,000 was adapted to neutral solution. The tunable and selective color change points brought an excellent feature of Ag NC-PEIs as visual pH indicators, which was flexible and applicable to a variety of environments. Besides, the ratios of absorbance at 415 nm and 268 nm of Ag NCs also showed linear relationships with pH variations. Therefore, there were three ways of this system for sensing pH values, including fluorescence assay, ultraviolet-visible measurement, and visual detection, suggesting that this tunable pH-sensing platform was more feasible, reliable, and accurate. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2015-01-14

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

  8. The general atomic and molecular electronic structure system HONDO: Version 7.0

    International Nuclear Information System (INIS)

    Dupuis, M.; Watts, J.D.; Villar, H.O.; Hurst, G.J.B.

    1989-01-01

    We describe a computer program for ab initio quantum mechanical calculations of atomic and molecular wavefunctions and energies. Capabilities for the calculation of energy gradients and second derivatives with respect to nuclear coordinates are provided for several types of wavefunctions. Calculations of many molecular properties based on the electron density are possible. The program contains automated algorithms for the determination of equilibrium structures, saddle points, reaction pathways, vibrational spectra including infrared and Raman intensities. We illustrate the capabilities of the program by highlighting research problems recently investigated with the present program. (orig.)

  9. Colorimetric biomimetic sensor systems based on molecularly imprinted polymer membranes for highly-selective detection of phenol in environmental samples

    Directory of Open Access Journals (Sweden)

    Sergeyeva T. A.

    2014-05-01

    Full Text Available Aim. Development of an easy-to-use colorimetric sensor system for fast and accurate detection of phenol in envi- ronmental samples. Methods. Technique of molecular imprinting, method of in situ polymerization of molecularly imprinted polymer membranes. Results. The proposed sensor is based on free-standing molecularly imprinted polymer (MIP membranes, synthesized by in situ polymerization, and having in their structure artificial binding sites capable of selective phenol recognition. The quantitative detection of phenol, selectively adsorbed by the MIP membranes, is based on its reaction with 4-aminoantipyrine, which gives a pink-colored product. The intensity of staining of the MIP membrane is proportional to phenol concentration in the analyzed sample. Phenol can be detected within the range 50 nM–10 mM with limit of detection 50 nM, which corresponds to the concentrations that have to be detected in natural and waste waters in accordance with environmental protection standards. Stability of the MIP-membrane-based sensors was assessed during 12 months storage at room temperature. Conclusions. The sensor system provides highly-selective and sensitive detection of phenol in both mo- del and real (drinking, natural, and waste water samples. As compared to traditional methods of phenol detection, the proposed system is characterized by simplicity of operation and can be used in non-laboratory conditions.

  10. In-cell protease assay systems based on trans-localizing molecular beacon proteins using HCV protease as a model system.

    Directory of Open Access Journals (Sweden)

    Jeong Hee Kim

    Full Text Available This study describes a sensitive in-cell protease detection system that enables direct fluorescence detection of a target protease and its inhibition inside living cells. This live-cell imaging system provides a fluorescent molecular beacon protein comprised of an intracellular translocation signal sequence, a protease-specific cleavage sequence, and a fluorescent tag sequence(s. The molecular beacon protein is designed to change its intracellular localization upon cleavage by a target protease, i.e., from the cytosol to a subcellular organelle or from a subcellular organelle to the cytosol. Protease activity can be monitored at the single cell level, and accordingly the entire cell population expressing the protease can be accurately enumerated. The clear cellular change in fluorescence pattern makes this system an ideal tool for various life science and drug discovery research, including high throughput and high content screening applications.

  11. A novel fully automated molecular diagnostic system (AMDS for colorectal cancer mutation detection.

    Directory of Open Access Journals (Sweden)

    Shiro Kitano

    Full Text Available BACKGROUND: KRAS, BRAF and PIK3CA mutations are frequently observed in colorectal cancer (CRC. In particular, KRAS mutations are strong predictors for clinical outcomes of EGFR-targeted treatments such as cetuximab and panitumumab in metastatic colorectal cancer (mCRC. For mutation analysis, the current methods are time-consuming, and not readily available to all oncologists and pathologists. We have developed a novel, simple, sensitive and fully automated molecular diagnostic system (AMDS for point of care testing (POCT. Here we report the results of a comparison study between AMDS and direct sequencing (DS in the detection of KRAS, BRAF and PI3KCA somatic mutations. METHODOLOGY/PRINCIPAL FINDING: DNA was extracted from a slice of either frozen (n = 89 or formalin-fixed and paraffin-embedded (FFPE CRC tissue (n = 70, and then used for mutation analysis by AMDS and DS. All mutations (n = 41 among frozen and 27 among FFPE samples detected by DS were also successfully (100% detected by the AMDS. However, 8 frozen and 6 FFPE samples detected as wild-type in the DS analysis were shown as mutants in the AMDS analysis. By cloning-sequencing assays, these discordant samples were confirmed as true mutants. One sample had simultaneous "hot spot" mutations of KRAS and PIK3CA, and cloning assay comfirmed that E542K and E545K were not on the same allele. Genotyping call rates for DS were 100.0% (89/89 and 74.3% (52/70 in frozen and FFPE samples, respectively, for the first attempt; whereas that of AMDS was 100.0% for both sample sets. For automated DNA extraction and mutation detection by AMDS, frozen tissues (n = 41 were successfully detected all mutations within 70 minutes. CONCLUSIONS/SIGNIFICANCE: AMDS has superior sensitivity and accuracy over DS, and is much easier to execute than conventional labor intensive manual mutation analysis. AMDS has great potential for POCT equipment for mutation analysis.

  12. Stability of therapeutic albumin solutions used for molecular adsorbent recirculating system-based liver dialysis.

    Science.gov (United States)

    De Bruyn, Tom; Meijers, Björn; Evenepoel, Pieter; Laub, Ruth; Willems, Ludo; Augustijns, Patrick; Annaert, Pieter

    2012-01-01

    Mounting evidence suggests beneficial effects of albumin dialysis-based liver support in patients suffering from acute-on-chronic liver failure. Molecular adsorbent recirculating system (MARS) is a nonbiological liver support device, based on the exchange of albumin-bound toxins between the patient's blood and a 20% human serum albumin solution in a secondary circuit. Bound toxins are continuously removed from the circulating albumin by exposure to activated charcoal and an ion-exchange resin. The aim of the present in vitro study was to determine the impact of exposure to charcoal and resin on the ligand binding properties of albumins, containing various levels of stabilizers and obtained from different suppliers (Baxter, CAF-DCF [Red Cross], and Sigma-Aldrich). Albumin binding properties were assessed by measuring equilibrium binding properties of warfarin, diazepam, and salicylate before and after incubation (for up to 7 h) with adsorbing materials; albumin-associated esterase-like activities were also determined. Notable changes in albumin binding upon incubation with adsorbing materials were only observed when using warfarin as a ligand. Affinity of warfarin for the Baxter and Sigma albumins showed a pronounced decrease (higher K(d) ) after the 1-7-h exposure to charcoal or resin. In the absence of adsorbing materials, similar effects were found, indicating that incubation time per se affects albumin binding properties. Following exposure to resin, Baxter albumin binding capacity (B(max)) increased about twofold. For albumin obtained from CAF-DCF, binding affinity and capacity for warfarin were constant under all conditions tested. Esterase-like activities associated with these albumins were either maintained or enhanced (up to 2.5-fold in case of Sigma albumin) following 7-h incubations with adsorbing materials. Our data suggest limited direct influence of the presence of stabilizers in therapeutic albumin solutions on baseline binding properties of human

  13. Molecular dynamics simulations of bio-nano systems with MBN Explorer

    DEFF Research Database (Denmark)

    Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2013-01-01

    We present results of molecular dynamics simulations performed using a multi-purpose computer code MBN Explorer. In particular we consider the process of laser induced acoustic desorption of lysine amino acids from the surface of a nickel foil. We analyze the rate of lysine desorption from...

  14. Ultrafast studies of dynamic & complex systems: Understanding molecular and ionization dynamics

    OpenAIRE

    Hockett, Paul

    2016-01-01

    Presentation given at the ITAMP workshop "Ultrafast atomic and molecular physics with cutting-edge light sources: New opportunities and challenges", held at Kansas State University, Nov. 2013.  A video of the presentation can be found on the ITAMP Youtube channel, https://www.youtube.com/watch?v=x8RWWDWZJpk

  15. Nanoindentation of ZrO{sub 2} and ZrO{sub 2}/Zr systems by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R., E-mail: sphil@mse.ufl.edu

    2017-04-01

    The deformation behaviors of cubic zirconia and a cubic zirconia thin film on top of an hcp zirconium substrate are investigated using molecular dynamics nanoindentation simulation. Interatomic interactions are described by the previously developed Charge Optimized Many Body (COMB) potential for the Zr-ZrO{sub 2}-O{sub 2} system. The load-displacement curves, deformation processes and hardnesses of zirconia and the zirconia/zirconium systems are characterized. In addition, by comparing with a previous nanoindentation simulation on zirconium, the effects of the zirconia layer on top on the mechanical properties of the zirconium substrate are determined.

  16. Molecular Genetic Characterization of Mutagenesis Using a Highly Sensitive Single-Stranded DNA Reporter System in Budding Yeast.

    Science.gov (United States)

    Chan, Kin

    2018-01-01

    Mutations are permanent alterations to the coding content of DNA. They are starting material for the Darwinian evolution of species by natural selection, which has yielded an amazing diversity of life on Earth. Mutations can also be the fundamental basis of serious human maladies, most notably cancers. In this chapter, I describe a highly sensitive reporter system for the molecular genetic analysis of mutagenesis, featuring controlled generation of long stretches of single-stranded DNA in budding yeast cells. This system is ~100- to ~1000-fold more susceptible to mutation than conventional double-stranded DNA reporters, and is well suited for generating large mutational datasets to investigate the properties of mutagens.

  17. Optimal control theory for quantum-classical systems: Ehrenfest molecular dynamics based on time-dependent density-functional theory

    International Nuclear Information System (INIS)

    Castro, A; Gross, E K U

    2014-01-01

    We derive the fundamental equations of an optimal control theory for systems containing both quantum electrons and classical ions. The system is modeled with Ehrenfest dynamics, a non-adiabatic variant of molecular dynamics. The general formulation, that needs the fully correlated many-electron wavefunction, can be simplified by making use of time-dependent density-functional theory. In this case, the optimal control equations require some modifications that we will provide. The abstract general formulation is complemented with the simple example of the H 2 + molecule in the presence of a laser field. (paper)

  18. Study of bond-energy variations in molecular systems under irradiation; Etude de la variation de l'energie de liaison dans les systemes moleculaires irradies

    Energy Technology Data Exchange (ETDEWEB)

    Naudet, G; Passe, S [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1968-07-01

    On the basis of experimental results selected from publications, the evolution of the bond energy of a molecular system under irradiation - leading to a more or less bound state - is studied. This variation of bond energy is then compared to the total bond energy of the initial system and to the energy absorbed in the system during the irradiation. This is done as a function of the nature of molecular system and the radiation spectrum and intensity. Our working method will first be explained, and the results obtained will then be given. (authors) [French] A l'aide de resultats experimentaux, selectionnes dans les publications, nous etudions l'evolution de l'energie de liaison d'un systeme moleculaire sous irradiation (evolution vers un etat plus ou moins lie), et nous comparons cette variation d'energie de liaison a l'energie totale de liaison du systeme initial et a l'energie absorbee dans le systeme au cours de l'irradiation. Ceci est fait en fonction de la nature du systeme moleculaire ainsi que du spectre et de l'intensite du rayonnement. Nous exposons d'abord notre methode de travail, puis les resultats obtenus. (auteurs)

  19. Light and redox switchable molecular components for molecular electronics.

    Science.gov (United States)

    Browne, Wesley R; Feringa, Ben L

    2010-01-01

    The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.

  20. Quantum mechanical modeling of molecular properties of systems with heavy-atoms in condensed phases and on interfaces

    International Nuclear Information System (INIS)

    Olejniczak, M.; Gomes, A.S.P.; Bast, R.

    2015-07-01

    We report an implementation of the nuclear magnetic resonance (NMR) shielding tensor in the frozen density embedding (FDE) scheme - in which the total system is divided into interacting subsystems - using the four-component (4c) relativistic Dirac-Coulomb (DC) Hamiltonian and the non-collinear spin density functional theory (SDFT). The formalism takes into account the magnetic balance between the large and the small components of molecular spinors and assures the gauge-origin independence of results. This implementation has been applied to hydrogen-bonded H 2 X---H 2 O complexes (X = Se, Te, Po) and compared with the super-molecular calculations and with the approach based on the integration of the magnetically induced current density vector. (authors)

  1. Molecular theory of partial molar volume and its applications to biomolecular systems

    Directory of Open Access Journals (Sweden)

    T.Imai

    2007-09-01

    Full Text Available The paial molar volume (PMV is a thermodynamic quantity which contains important information about the solute-solvent interactions as well as the solute structure in solution.Additionally, the PMV is the most essential quantity in the analysis of the pressure effect on chemical reactions. This aicle reviews the recent developments in molecular theories of the PMV, especially the reference interaction site model (RISMtheory of molecular liquids and its three-dimensional generalization version (3D-RISM, which are combined with the Kirkwood-Buff solution theory to calculate the PMV. This aicle also introduces our recent applications of the theory to some interesting issues concerning the PMV of biomolecules. In addition, theoretical representations of the effects of intramolecular fluctuation on the PMV, which are significant for biomacromolecules, are briefly discussed.

  2. Method and system for gas flow mitigation of molecular contamination of optics

    Science.gov (United States)

    Delgado, Gildardo; Johnson, Terry; Arienti, Marco; Harb, Salam; Klebanoff, Lennie; Garcia, Rudy; Tahmassebpur, Mohammed; Scott, Sarah

    2018-01-23

    A computer-implemented method for determining an optimized purge gas flow in a semi-conductor inspection metrology or lithography apparatus, comprising receiving a permissible contaminant mole fraction, a contaminant outgassing flow rate associated with a contaminant, a contaminant mass diffusivity, an outgassing surface length, a pressure, a temperature, a channel height, and a molecular weight of a purge gas, calculating a flow factor based on the permissible contaminant mole fraction, the contaminant outgassing flow rate, the channel height, and the outgassing surface length, comparing the flow factor to a predefined maximum flow factor value, calculating a minimum purge gas velocity and a purge gas mass flow rate from the flow factor, the contaminant mass diffusivity, the pressure, the temperature, and the molecular weight of the purge gas, and introducing the purge gas into the semi-conductor inspection metrology or lithography apparatus with the minimum purge gas velocity and the purge gas flow rate.

  3. Temperature dependence of the anisotropy of fluorescence in ring molecular systems

    International Nuclear Information System (INIS)

    Herman, Pavel; Barvik, Ivan

    2007-01-01

    The time dependence of the anisotropy of fluorescence after an impulsive excitation in the molecular ring (resembling the B850 ring of the purple bacterium Rhodopseudomonas acidophila) is calculated. Fast fluctuations of the environment are simulated by dynamic disorder and slow fluctuations by uncorrelated static disorder. Without dynamic disorder modest degrees of static disorder are sufficient to cause the experimentally found initial drop of the anisotropy on a sub-100 fs time scale. In the present investigation we are comparing results for the time-dependent optical anisotropy of the molecular ring for four models of the uncorrelated static disorder: Gaussian disorder in the local energies (model A), Gaussian disorder in the transfer integrals (model B), Gaussian disorder in radial positions of molecules (model C) and Gaussian disorder in angular positions of molecules (model D). Both types of disorder-static and dynamic-are taken into account simultaneously

  4. Nonreactive spreading at high-temperature revisited for metal systems via molecular dynamics.

    Science.gov (United States)

    Benhassine, M; Saiz, E; Tomsia, A P; De Coninck, J

    2009-10-06

    The spreading for Cu and Ag droplets on top of a rigid solid surface modeling Mo is herewith considered via molecular dynamics. The dynamics of the base radius and the contact angle are recorded and fitted using the molecular-kinetic theory. A method is described to determine for liquid metals at the microscopic level the parameters appearing in this theory. These microscopic parameters are calculated directly in the simulations and compared to the fitted values. The agreement between the fitted values and the calculated ones shows that the dissipation of energy within the drop is caused primarily by the friction of liquid atoms over the substrate. This validation supports the understanding of the mechanisms controlling the spreading of liquid metals which, up to now, were based on experimental data and fitting procedures.

  5. Toward a molecular programming language for algorithmic self-assembly

    Science.gov (United States)

    Patitz, Matthew John

    Self-assembly is the process whereby relatively simple components autonomously combine to form more complex objects. Nature exhibits self-assembly to form everything from microscopic crystals to living cells to galaxies. With a desire to both form increasingly sophisticated products and to understand the basic components of living systems, scientists have developed and studied artificial self-assembling systems. One such framework is the Tile Assembly Model introduced by Erik Winfree in 1998. In this model, simple two-dimensional square 'tiles' are designed so that they self-assemble into desired shapes. The work in this thesis consists of a series of results which build toward the future goal of designing an abstracted, high-level programming language for designing the molecular components of self-assembling systems which can perform powerful computations and form into intricate structures. The first two sets of results demonstrate self-assembling systems which perform infinite series of computations that characterize computably enumerable and decidable languages, and exhibit tools for algorithmically generating the necessary sets of tiles. In the next chapter, methods for generating tile sets which self-assemble into complicated shapes, namely a class of discrete self-similar fractal structures, are presented. Next, a software package for graphically designing tile sets, simulating their self-assembly, and debugging designed systems is discussed. Finally, a high-level programming language which abstracts much of the complexity and tedium of designing such systems, while preventing many of the common errors, is presented. The summation of this body of work presents a broad coverage of the spectrum of desired outputs from artificial self-assembling systems and a progression in the sophistication of tools used to design them. By creating a broader and deeper set of modular tools for designing self-assembling systems, we hope to increase the complexity which is

  6. Effects of Organics on the Adsorption and Mobility of Metal Cations in Clay Systems: Computational Molecular Modeling Approach

    International Nuclear Information System (INIS)

    Kalinichev, Andrey G.; Ngouana Wakou, Brice F.; Loganathan, Narasimhan

    2013-01-01

    Understanding and prediction of many natural and anthropogenic environmental processes ultimately depend on a fundamental understanding of the chemistry occurring at the mineral-fluid inter-faces. Clay-related minerals and natural organic matter (NOM) are ubiquitous in the environment, and metal-NOM complexation induces strong correlations between the NOM concentration in water and the capacity of clay particles to bind metals, thus affecting their speciation, solubility and toxicity in the environment. Despite significant geochemical, environmental and technological interest, the molecular-level mechanisms and dynamics of the physical and chemical processes involving NOM are not yet well understood. In this presentation we compare three different molecular dynamics (MD) computer simulations of metal-NOM complexation in aqueous solutions. The simulation results indicate that despite some obvious quantitative variations in the computed values depending on the size of the simulated system and on the parameters of the force field models used, all three simulations are quite robust and consistent. In particular, approximately 35-50% of Ca 2+ ions in all simulations are associated with the carboxylic groups of NOM at near-neutral pH. The stability of bidentate-coordinated contact ion pair complexes is also always strongly preferred. Easy association of metal cations with negatively charged NOM functional groups and negatively charged clay surfaces allows us to predict that cationic bridging could be the most probable mechanism of NOM association with clays in natural environments. New MD simulations are currently in progress to quantitatively assess these predictions on a molecular scale for nuclear waste disposal applications. New larger-scale clay models incorporate a more realistic representation of the structural and compositional disorder of natural illites and smectites and employ CLAYFF - a fully flexible general force field suitable for the molecular simulations

  7. Correction of auto interaction in the formalism of the local spin density: molecular systems

    International Nuclear Information System (INIS)

    Figueiredo, S.K. de.

    1987-01-01

    The auto-insertion correction proposed by Perdew and Zunger is introduced in the multiple scattering. The orbital spin relaxation is analyzed and this model is applied to the molecules = CH 4 , SiH 4 , GeH 4 as well as for the molecular compound GaAs with seventeen atoms in the [1Ga4As12Ga] configuration. (A.C.A.S.) [pt

  8. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints.

    Science.gov (United States)

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M

    2015-06-01

    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits.

  9. Localized orbitals vs. pseudopotential-plane waves basis sets: performances and accuracy for molecular magnetic systems

    International Nuclear Information System (INIS)

    Massobrio, C.; Ruiz, E.

    2003-01-01

    Density functional theory, in combination with a) a careful choice of the exchange-correlation part of the total energy and b) localized basis sets for the electronic orbital, has become the method of choice for calculating the exchange-couplings in magnetic molecular complexes. Orbital expansion on plane waves can be seen as an alternative basis set especially suited to allow optimization of newly synthesized materials of unknown geometries. However, little is known on the predictive power of this scheme to yield quantitative values for exchange coupling constants J as small as a few hundredths of eV (50-300 cm -1 ). We have used density functional theory and a plane waves basis set to calculate the exchange couplings J of three homodinuclear Cu-based molecular complexes with experimental values ranging from +40 cm -1 to -300 cm -1 . The plane waves basis set proves as accurate as the localized basis set, thereby suggesting that this approach can be reliably employed to predict and rationalize the magnetic properties of molecular-based materials. (author)

  10. A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease

    Science.gov (United States)

    Huan, Tianxiao; Zhang, Bin; Wang, Zhi; Joehanes, Roby; Zhu, Jun; Johnson, Andrew D.; Ying, Saixia; Munson, Peter J.; Raghavachari, Nalini; Wang, Richard; Liu, Poching; Courchesne, Paul; Hwang, Shih-Jen; Assimes, Themistocles L.; McPherson, Ruth; Samani, Nilesh J.; Schunkert, Heribert; Meng, Qingying; Suver, Christine; O'Donnell, Christopher J.; Derry, Jonathan; Yang, Xia; Levy, Daniel

    2013-01-01

    Objective Genetic approaches have identified numerous loci associated with coronary heart disease (CHD). The molecular mechanisms underlying CHD gene-disease associations, however, remain unclear. We hypothesized that genetic variants with both strong and subtle effects drive gene subnetworks that in turn affect CHD. Approach and Results We surveyed CHD-associated molecular interactions by constructing coexpression networks using whole blood gene expression profiles from 188 CHD cases and 188 age- and sex-matched controls. 24 coexpression modules were identified including one case-specific and one control-specific differential module (DM). The DMs were enriched for genes involved in B-cell activation, immune response, and ion transport. By integrating the DMs with altered gene expression associated SNPs (eSNPs) and with results of GWAS of CHD and its risk factors, the control-specific DM was implicated as CHD-causal based on its significant enrichment for both CHD and lipid eSNPs. This causal DM was further integrated with tissue-specific Bayesian networks and protein-protein interaction networks to identify regulatory key driver (KD) genes. Multi-tissue KDs (SPIB and TNFRSF13C) and tissue-specific KDs (e.g. EBF1) were identified. Conclusions Our network-driven integrative analysis not only identified CHD-related genes, but also defined network structure that sheds light on the molecular interactions of genes associated with CHD risk. PMID:23539213

  11. The Challenges of Recombinant Endostatin in Clinical Application: Focus on the Different Expression Systems and Molecular Bioengineering

    Directory of Open Access Journals (Sweden)

    Abbas Mohajeri

    2017-04-01

    Full Text Available Angiogenesis plays an essential role in rapid growing and metastasis of the tumors. Inhibition of angiogenesis is a putative strategy for cancer therapy. Endostatin (Es is an attractive anti-angiogenesis protein with some clinical application challenges including; short half-life, instability in serum and requirement to high dosage. Therefore, production of recombinant endostatin (rEs is necessary in large scale. The production of rEs is difficult because of its structural properties and is high-cost. Therefore, this review focused on the different expression systems that involved in rEs production including; mammalian, baculovirus, yeast, and Escherichia coli (E. coli expression systems. The evaluating of the results of different expression systems declared that none of the mentioned systems can be considered to be generally superior to the other. Meanwhile with considering the advantages and disadvantage of E. coli expression system compared with other systems beside the molecular properties of Es, E. coli expression system can be a preferred expression system for expressing of the Es in large scale. Also, the molecular bioengineering and sustained release formulations that lead to improving of its stability and bioactivity will be discussed. Point mutation (P125A of Es, addition of RGD moiety or an additional zinc biding site to N-terminal of Es , fusing of Es to anti-HER2 IgG or heavy-chain of IgG, and finally loading of the endostar by PLGA and PEG- PLGA nanoparticles and gold nano-shell particles are the effective bioengineering methods to overcome to clinical changes of endostatin.

  12. A Pilot-Scale System for Carbon Molecular Sieve Hollow Fiber Membrane Manufacturing

    KAUST Repository

    Karvan, O.; Johnson, J. R.; Williams, P. J.; Koros, W. J.

    2012-01-01

    research on these materials with a variety of applications being studied. The results from a pilot-scale CMS production system are presented. This system was designed based on extensive laboratory research, and hollow fiber membranes produced in this system

  13. Functionalized Nanolipobubbles Embedded Within a Nanocomposite Hydrogel: a Molecular Bio-imaging and Biomechanical Analysis of the System.

    Science.gov (United States)

    Mufamadi, Maluta S; Choonara, Yahya E; Kumar, Pradeep; du Toit, Lisa C; Modi, Girish; Naidoo, Dinesh; Iyuke, Sunny E; Pillay, Viness

    2017-04-01

    The purpose of this study was to explore the use of molecular bio-imaging systems and biomechanical dynamics to elucidate the fate of a nanocomposite hydrogel system prepared by merging FITC-labeled nanolipobubbles within a cross-linked hydrogel network. The nanocomposite hydrogel system was characterized by size distribution analysis and zeta potential as well as shears thinning behavior, elastic modulus (G'), viscous loss moduli (G"), TEM, and FTIR. In addition, molecular bio-imaging via Vevo ultrasound and Cell-viZio techniques evaluated the stability and distribution of the nanolipobubbles within the cross-linked hydrogel. FITC-labeled and functionalized nanolipobubbles had particle sizes between 135 and 158 nm (PdI = 0.129 and 0.190) and a zeta potential of -34 mV. TEM and ultrasound imaging revealed the uniformity and dimensional stability of the functionalized nanolipobubbles pre- and post-embedment into the cross-linked hydrogel. Biomechanical characterization of the hydrogel by shear thinning behavior was governed by the polymer concentration and the cross-linker, glutaraldehyde. Ultrasound analysis and Cell-viZio bio-imaging were highly suitable to visualize the fluorescent image-guided nanolipobubbles and their morphology post-embedment into the hydrogel to form the NanoComposite system. Since the nanocomposite is intended for targeted treatment of neurodegenerative disorders, the distribution of the functionalized nanolipobubbles into PC12 neuronal cells was also ascertained via confocal microscopy. Results demonstrated effective release and localization of the nanolipobubbles within PC12 neuronal cells. The molecular structure of the synthetic surface peptide remained intact for an extended period to ensure potency for targeted delivery from the hydrogel ex vivo. These findings provide further insight into the properties of nanocomposite hydrogels for specialized drug delivery.

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

    Science.gov (United States)

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

    2018-01-18

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

  15. Molecular replacement then and now

    International Nuclear Information System (INIS)

    Scapin, Giovanna

    2013-01-01

    A brief overview, with examples, of the evolution of molecular-replacement methods and models over the past few years is presented. The ‘phase problem’ in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962 ▶), Acta Cryst.15, 24–31]. The term ‘molecular replacement’ was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972 ▶), The Molecular Replacement Method. New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the ‘best’ search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to

  16. epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens

    Directory of Open Access Journals (Sweden)

    González-Candelas Fernando

    2007-04-01

    Full Text Available Abstract Background Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. Results From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. Conclusion epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the

  17. Ultra-sensitive molecular MRI of cerebrovascular cell activation enables early detection of chronic central nervous system disorders

    International Nuclear Information System (INIS)

    Montagne, Axel; Gauberti, Maxime; Jullienne, Amandine; Briens, Aurelien; Docagne, Fabian; Vivien, Denis; Maubert, Eric; Macrez, Richard; Defer, Gilles; Raynaud, Jean-Sebastien; Louin, Gaelle; Buisson, Alain; Haelewyn, Benoit

    2012-01-01

    Since endothelial cells can be targeted by large contrast-carrying particles, molecular imaging of cerebrovascular cell activation is highly promising to evaluate the underlying inflammation of the central nervous system (CNS). In this study, we aimed to demonstrate that molecular magnetic resonance imaging (MRI) of cerebrovascular cell activation can reveal CNS disorders in the absence of visible lesions and symptoms. To this aim, we optimized contrast carrying particles targeting vascular cell adhesion molecule-1 and MRI protocols through both in vitro and in vivo experiments. Although, pre-contrast MRI images failed to reveal the ongoing pathology, contrast-enhanced MRI revealed hypoperfusion-triggered CNS injury in vascular dementia, unmasked amyloid-induced cerebrovascular activation in Alzheimer's disease and allowed monitoring of disease activity during experimental autoimmune encephalomyelitis. Moreover, contrast-enhanced MRI revealed the cerebrovascular cell activation associated with known risk factors of CNS disorders such as peripheral inflammation, ethanol consumption, hyperglycemia and aging. By providing a dramatically higher sensitivity than previously reported methods and molecular contrast agents, the technology described in the present study opens new avenues of investigation in the field of neuro-inflammation. (authors)

  18. Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

    Science.gov (United States)

    König, Gerhard; Mei, Ye; Pickard, Frank C; Simmonett, Andrew C; Miller, Benjamin T; Herbert, John M; Woodcock, H Lee; Brooks, Bernard R; Shao, Yihan

    2016-01-12

    A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.

  19. Sophistication of 14C measurement at JAEA-AMS-MUTSU. Attempt on a small quantity of sample

    International Nuclear Information System (INIS)

    Tanaka, Takayuki; Kabuto, Shoji; Kinoshita, Naoki; Yamamoto, Nobuo

    2010-01-01

    In the investigations on substance dynamics using the molecular weight and chemical fractionation, the utilization of 14 C measurement by an accelerator mass spectrometry (AMS) have started. As a result of the fractionation, sample contents required for AMS measurement have been downsized. We expect that this trend toward a small quantity of sample will be steadily accelerated in the future. As 14 C measurement by AMS established at Mutsu office require about 2 mg of sample content at present, our AMS lags behind the others in the trend. We try to downsize the needed sample content for 14 C measurement by our AMS. In this study, we modified the shape of the target-piece in which the sample is packed and which is regularly needed to radiocarbon measurement by our AMS. Moreover, we improved on the apparatus needed to pack the sample. As a result of the improvement, we revealed that it is possible to measure the 14 C using our AMS even by the amount of the sample of about 0.5 mg. (author)

  20. The influence of molecular layers of amines on the hydraulic resistance of piping systems and power plant equipment

    Energy Technology Data Exchange (ETDEWEB)

    Ryzhenkov, Viacheslav A.; Ryzhenkov, Artem V. [Moscow Power Engineering Institute / Technical Univ. (Russian Federation). Dept. of Industrial Heat and Power Systems; Petrova, Tamara I. [Moscow Power Engineering Institute / Technical Univ. (Russian Federation). Water and Fuel Technology Dept.

    2012-07-15

    The current state of pipeline systems and power equipment has a high accident rate due to intense corrosion, the accumulation of deposits on heat and in-line transfer surfaces, and high hydraulic resistance. Analysis and synthesis of published results shows that the solution to improving the efficiency of pipeline systems and power equipment can be approached from two directions: (i) the impact on the properties of transported media and (ii) changes in the properties of functional surfaces of pipelines and equipment. Improving the ''quality'' of the technological agents involves very substantial capital and operating costs, so the most promising way is to modify the surface properties. Studies conducted at the National Research University MPEI showed that these problems are solved more effectively by means of molecular layers of adsorbed amines on the functional surfaces of pipes and equipment. When present in a certain way with the optimal number of molecular amine layers, these significantly alter the surface properties of conventional structural materials, which leads to very substantial improvement in the hydrodynamic characteristics: reduction of the hydraulic resistance of pipelines and equipment (up to 40 %), almost complete stoppage of corrosion processes (up to 7 times), and a multiple (up to 10-fold) reduction in the rate of deposit accumulation. The method of adsorption of molecular amine layers and the equipment for its implementation developed on the basis of this research will not only reduce flow resistance, but will also significantly improve the operating efficiency of pipeline systems and power equipment generally. (orig.)

  1. Computation of Ground-State Properties in Molecular Systems: Back-Propagation with Auxiliary-Field Quantum Monte Carlo.

    Science.gov (United States)

    Motta, Mario; Zhang, Shiwei

    2017-11-14

    We address the computation of ground-state properties of chemical systems and realistic materials within the auxiliary-field quantum Monte Carlo method. The phase constraint to control the Fermion phase problem requires the random walks in Slater determinant space to be open-ended with branching. This in turn makes it necessary to use back-propagation (BP) to compute averages and correlation functions of operators that do not commute with the Hamiltonian. Several BP schemes are investigated, and their optimization with respect to the phaseless constraint is considered. We propose a modified BP method for the computation of observables in electronic systems, discuss its numerical stability and computational complexity, and assess its performance by computing ground-state properties in several molecular systems, including small organic molecules.

  2. Quantum mechanical study of molecular collisions at ultra-low energy: applications to alkali and alkaline-earth systems

    International Nuclear Information System (INIS)

    Quemener, G.

    2006-10-01

    In order to investigate the collisional processes which occur during the formation of molecular Bose-Einstein condensates, a time-independent quantum mechanical formalism, based on hyperspherical coordinates, has been applied to the study of atom-diatom dynamics at ultra-low energies. We present theoretical results for three alkali systems, each composed of lithium, sodium or potassium atoms, and for an alkaline-earth system composed of calcium atoms. We also study dynamics at large and positive atom-atom scattering length. Evidence for the suppression of inelastic processes in a fermionic system is given, as well as a linear relation between the atom-diatom scattering length and the atom-atom scattering length. (author)

  3. Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System

    DEFF Research Database (Denmark)

    Rapin, N.; Lund, Ole; Bernaschi, M.

    2010-01-01

    potential measurements, for assessing molecular binding in the context of immune complexes. We benchmark the resulting model by simulating a classical immunization experiment that reproduces the development of immune memory. We also investigate the role of major histocompatibility complex (MHC) haplotype...... proliferate more than any other. These results show that the simulator produces dynamics that are stable and consistent with basic immunological knowledge. We believe that the combination of genomic information and simulation of the dynamics of the immune system, in one single tool, can offer new perspectives......We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response, C-IMMSIM, such that it represents pathogens, as well...

  4. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure.

    Science.gov (United States)

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-05-17

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

  5. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

    Science.gov (United States)

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-05-01

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

  6. Visualization system: animation of the dynamic evolution of the molecular hydrogen cloud during its gravitational collapse in 3D

    International Nuclear Information System (INIS)

    Duarte P, R.; Klapp E, J.; Arreaga D, G.

    2006-01-01

    The results of a group of numeric simulations and a region of interest form a molecular hydrogen cloud that collapses under the action of their own force of graveness. For they are believed it two models the constant one and the gaussian with the profile of the density of the initial cloud and a barotropic equation of state that it allows the iso thermic change to adiabatic. For each pattern two values of critical density are used, a spectra of density interferences, obtaining a binary system, tertiary or even a quaternary one. The necessary programs explained in the methodology to generate the visualizations of the models are generated. (Author)

  7. Design of supramolecular ordered systems for mesoscopic colloids and molecular composites. Progress report, November 10, 1993--June 10, 1994

    Energy Technology Data Exchange (ETDEWEB)

    1995-01-01

    During this reporting period, the authors group has been active in five areas of research: (1) improvements on their x-ray instrumentation at the SUNY Beamline, National Synchrotron Light Source (NSLS) so that they can perform new experiments which are not accessible otherwise; (2) characterization of functionalized hairy rod polymers designed for studying the macromolecular structures in molecular composites; (3) investigation of supramolecular ordered systems composed mainly of block copolymers from dilute to concentrated solutions, including the gel state; (4) evolution of crystalline structures in polymer blends and melts; and (5) multiphase structure of segment polyurethanes.

  8. Atomic and molecular physics - Ions in solids - Laser systems. Courses, corrected exercises and problems Level M1/M2

    International Nuclear Information System (INIS)

    Cremer, Georgette-Laura; Moncorge, Richard; Chesnel, Jean-Yves; Adoui, Lamri; Lelievre, Gerard

    2010-01-01

    This document proposes the table of contents and a brief presentation of a course book for students in atomic and molecular physics. After some generalities on energy quantification and on photon momentum / Compton Effect, the different chapters address topics like hydrogen and helium atoms, alkalis, alkaline-earth, atoms with several valence electrons, the atom-radiation interaction, molecule and ion spectroscopy in solids, and the most significant laser systems using an active media based on atoms, ions or molecules in a diluted environment. Each chapter contains exercises and problems

  9. Performance of Four Transport and Storage Systems for Molecular Detection of Multidrug-Resistant Tuberculosis

    Science.gov (United States)

    Rabodoarivelo, Marie Sylvianne; Imperiale, Bélen; andrianiavomikotroka, Rina; Brandao, Angela; Kumar, Parveen; Singh, Sarman; Ferrazoli, Lucilaine; Morcillo, Nora; Rasolofo, Voahangy; Palomino, Juan Carlos; Vandamme, Peter; Martin, Anandi

    2015-01-01

    Background Detection of drug-resistant tuberculosis is essential for the control of the disease but it is often hampered by the limitation of transport and storage of samples from remote locations to the reference laboratory. We performed a retrospective field study to evaluate the performance of four supports enabling the transport and storage of samples to be used for molecular detection of drug resistance using the GenoType MTBDRplus. Methods Two hundred Mycobacterium tuberculosis strains were selected and spotted on slides, FTA cards, GenoCards, and in ethanol. GenoType MTBDRplus was subsequently performed with the DNA extracted from these supports. Sensitivity and specificity were calculated and compared to the results obtained by drug susceptibility testing. Results For all supports, the overall sensitivity and specificity for detection of resistance to RIF was between 95% and 100%, and for INH between 95% and 98%. Conclusion The four transport and storage supports showed a good sensitivity and specificity for the detection of resistance to RIF and INH in M. tuberculosis strains using the GenoType MTBDRplus. These supports can be maintained at room temperature and could represent an important alternative cost-effective method useful for rapid molecular detection of drug-resistant TB in low-resource settings. PMID:26431352

  10. Localized orbitals vs. pseudopotential-plane waves basis sets: performances and accuracy for molecular magnetic systems

    CERN Document Server

    Massobrio, C

    2003-01-01

    Density functional theory, in combination with a) a careful choice of the exchange-correlation part of the total energy and b) localized basis sets for the electronic orbital, has become the method of choice for calculating the exchange-couplings in magnetic molecular complexes. Orbital expansion on plane waves can be seen as an alternative basis set especially suited to allow optimization of newly synthesized materials of unknown geometries. However, little is known on the predictive power of this scheme to yield quantitative values for exchange coupling constants J as small as a few hundredths of eV (50-300 cm sup - sup 1). We have used density functional theory and a plane waves basis set to calculate the exchange couplings J of three homodinuclear Cu-based molecular complexes with experimental values ranging from +40 cm sup - sup 1 to -300 cm sup - sup 1. The plane waves basis set proves as accurate as the localized basis set, thereby suggesting that this approach can be reliably employed to predict and r...

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

    Directory of Open Access Journals (Sweden)

    Anne Albrecht

    2017-01-01

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

  12. Molecular mechanism and function of CD40/CD40L engagement in the immune system.

    Science.gov (United States)

    Elgueta, Raul; Benson, Micah J; de Vries, Victor C; Wasiuk, Anna; Guo, Yanxia; Noelle, Randolph J

    2009-05-01

    During the generation of a successful adaptive immune response, multiple molecular signals are required. A primary signal is the binding of cognate antigen to an antigen receptor expressed by T and B lymphocytes. Multiple secondary signals involve the engagement of costimulatory molecules expressed by T and B lymphocytes with their respective ligands. Because of its essential role in immunity, one of the best characterized of the costimulatory molecules is the receptor CD40. This receptor, a member of the tumor necrosis factor receptor family, is expressed by B cells, professional antigen-presenting cells, as well as non-immune cells and tumors. CD40 binds its ligand CD40L, which is transiently expressed on T cells and other non-immune cells under inflammatory conditions. A wide spectrum of molecular and cellular processes is regulated by CD40 engagement including the initiation and progression of cellular and humoral adaptive immunity. In this review, we describe the downstream signaling pathways initiated by CD40 and overview how CD40 engagement or antagonism modulates humoral and cellular immunity. Lastly, we discuss the role of CD40 as a target in harnessing anti-tumor immunity. This review underscores the essential role CD40 plays in adaptive immunity.

  13. Properties of aqueous systems relevant to the SCWR via molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kallikragas, D. [Trent Univ., Dept. of Chemistry, Peterborough, Ontario (Canada); Guzonas, D. [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada); Svishchev, I., E-mail: isvishchev@trentu.ca [Trent Univ., Dept. of Chemistry, Peterborough, Ontario (Canada)

    2015-06-15

    Supercritical water (SCW) is the intended heat transfer fluid in the proposed GEN-IV supercritical water cooled reactor (SCWR). The oxidative environment poses challenges in choosing appropriate design materials and understanding the behaviour of SCW at the nanoscale within crevices of the passivation layer is needed for developing a control strategy to minimize corrosion. Molecular dynamics simulations have been employed to investigate molecular structure and diffusion of water and chloride in nanometer-spaced iron hydroxide surfaces. Results demonstrate that water is more likely to accumulate on the surface at low-density conditions. The effect of confinement on the water structure diminishes with as little as 20 Å of surface separation. Clustering and the accumulation of water at the surface imply that the SCWR will be most susceptible to pitting corrosion and stress corrosion cracking. A parameterized equation is provided that gives the diffusion coefficients of {sub O2}, H{sub 2}, and OH radical in high temperature and SCW. (author)

  14. Dialing long distance : communications to northern operations like the MGP require sophisticated satellite networks for voice, data

    Energy Technology Data Exchange (ETDEWEB)

    Cook, D.

    2006-04-15

    Telecommunications will play a major role in the construction of the Mackenzie Gas Project due to the remoteness of its location and the volume of communication data required to support the number of people involved and the amount of construction activity. While suppliers for communications tools have not yet been identified, initial telecommunications plans call for the installation of communication equipment at all camps, major facility sites and construction locations. Equipment will be housed in self-contained, climate-controlled buildings called telecommunication service modules (TSMs), which will be connected to each other as well as to existing public communications networks. The infrastructure will support telephone and fax systems; Internet and electronic mail services; multiple channel very high frequency radios; air-to-ground communication at airstrips and helipads; ship-to-shore at barge landings; closed circuit television; satellite community antenna television; CBC radio broadcast; public address systems; security systems; and supervisory control and data acquisition (SCADA) systems. An Internet Protocol (IP) network with a voice telephone system will be implemented along with a geostationary orbit satellite network. Satellite servers and real-time data services will be used. Car kits that allow call and battery-operated self-contained telemetry devices designed to communicate via a satellite system have been commissioned for the project that are capable of providing cost-efficient and reliable asset tracking and fleet management in remote regions and assisting in deployment requirements. It was concluded that many of today's mega-projects are the driving factors behind new telecommunications solutions in remote areas. 1 fig.

  15. Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing.

    Science.gov (United States)

    Olvera, Alex; Busquets, Núria; Cortey, Marti; de Deus, Nilsa; Ganges, Llilianne; Núñez, José Ignacio; Peralta, Bibiana; Toskano, Jennifer; Dolz, Roser

    2010-05-01

    Changes in livestock production systems in recent years have altered the presentation of many diseases resulting in the need for more sophisticated control measures. At the same time, new molecular assays have been developed to support the diagnosis of animal viral disease. Nucleotide sequences generated by these diagnostic techniques can be used in phylogenetic analysis to infer phenotypes by sequence homology and to perform molecular epidemiology studies. In this review, some key elements of phylogenetic analysis are highlighted, such as the selection of the appropriate neutral phylogenetic marker, the proper phylogenetic method and different techniques to test the reliability of the resulting tree. Examples are given of current and future applications of phylogenetic reconstructions in viral livestock diseases. Copyright 2009 Elsevier Ltd. All rights reserved.

  16. The 4-particle hydrogen-anti-hydrogen system revisited. Twofold molecular Hamiltonian symmetry and natural atom anti-hydrogen

    International Nuclear Information System (INIS)

    Van Hooydonk, G.

    2005-01-01

    The historical importance of the original quantum mechanical bond theory proposed by Heitler and London in 1927 as well as its pitfalls are reviewed. Modern ab initio treatments of H-H-bar systems are inconsistent with the logic behind algebraic Hamiltonians H ± = H 0 ± ΔH for charge-symmetrical and charge-asymmetrical 4 unit charge systems like H 2 and HH-bar. Their eigenvalues are exactly those of 1927 Heitler-London (HL) theory. Since these 2 Hamiltonians are mutually exclusive, only the attractive one can apply for stable natural molecular H 2 . A wrong choice leads to problems with anti-atom H-bar. In line with earlier results on band and line spectra, we now prove that HL chose the wrong Hamiltonian for H 2 . Their theory explains the stability of attractive system H 2 with a repulsive Hamiltonian H 0 + ΔH instead of with the attractive one H 0 - ΔH, representative for charge-asymmetrical system HH-bar. A new second order symmetry effect is detected in this attractive Hamiltonian, which leads to a 3-dimensional structure for the 4-particle system. Repulsive HL Hamiltonian H + applies at long range but at the critical distance, attractive charge-inverted Hamiltonian H - takes over and leads to bond H 2 but in reality, HH-bar, for which we give an analytical proof. This analysis confirms and generalizes an earlier critique of the wrong long range behavior of HL-theory by Bingel, Preuss and Schmidtke and by Herring. Another wrong asymptote choice in the past also applies for atomic anti-hydrogen H-bar, which has hidden the Mexican hat potential for natural hydrogen. This generic solution removes most problems, physicists and chemists experience with atomic H-bar and molecular HH-bar, including the problem with antimatter in the Universe. (author)

  17. A Systems Biology Analysis Unfolds the Molecular Pathways and Networks of Two Proteobacteria in Spaceflight and Simulated Microgravity Conditions.

    Science.gov (United States)

    Roy, Raktim; Shilpa, P Phani; Bagh, Sangram

    2016-09-01

    Bacteria are important organisms for space missions due to their increased pathogenesis in microgravity that poses risks to the health of astronauts and for projected synthetic biology applications at the space station. We understand little about the effect, at the molecular systems level, of microgravity on bacteria, despite their significant incidence. In this study, we proposed a systems biology pipeline and performed an analysis on published gene expression data sets from multiple seminal studies on Pseudomonas aeruginosa and Salmonella enterica serovar Typhimurium under spaceflight and simulated microgravity conditions. By applying gene set enrichment analysis on the global gene expression data, we directly identified a large number of new, statistically significant cellular and metabolic pathways involved in response to microgravity. Alteration of metabolic pathways in microgravity has rarely been reported before, whereas in this analysis metabolic pathways are prevalent. Several of those pathways were found to be common across studies and species, indicating a common cellular response in microgravity. We clustered genes based on their expression patterns using consensus non-negative matrix factorization. The genes from different mathematically stable clusters showed protein-protein association networks with distinct biological functions, suggesting the plausible functional or regulatory network motifs in response to microgravity. The newly identified pathways and networks showed connection with increased survival of pathogens within macrophages, virulence, and antibiotic resistance in microgravity. Our work establishes a systems biology pipeline and provides an integrated insight into the effect of microgravity at the molecular systems level. Systems biology-Microgravity-Pathways and networks-Bacteria. Astrobiology 16, 677-689.

  18. The Henry Ford production system: LEAN process redesign improves service in the molecular diagnostic laboratory: a paper from the 2008 William Beaumont hospital symposium on molecular pathology.

    Science.gov (United States)

    Cankovic, Milena; Varney, Ruan C; Whiteley, Lisa; Brown, Ron; D'Angelo, Rita; Chitale, Dhananjay; Zarbo, Richard J

    2009-09-01

    Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here, we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN production. Our goal was to complete greater than 90% of the molecular tests in less than 3 days. The project required cooperation from different laboratory disciplines as well as individuals outside of the laboratory. The redesigned processes involved defining and standardizing the protocols and approaching blood and tissue specimens as analytes for molecular testing. The LEAN process resulted in fewer steps, approaching the ideal of a one-piece flow for specimens through collection/retrieval, transport, and different aspects of the testing process. The outcome of introducing the LEAN process has been a 44% reduction in molecular test turnaround time for tissue specimens, from an average of 2.7 to 1.5 days. In addition, extending LEAN work principles to the clinician suppliers has resulted in a markedly increased number of properly collected and shipped blood specimens (from 50 to 87%). These continuous quality improvements were accomplished by empowered workers in a blame-free environment and are now being sustained with minimal management involvement.

  19. System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management.

    Science.gov (United States)

    Kang, Wenjun; Kadri, Sabah; Puranik, Rutika; Wurst, Michelle N; Patil, Sushant A; Mujacic, Ibro; Benhamed, Sonia; Niu, Nifang; Zhen, Chao Jie; Ameti, Bekim; Long, Bradley C; Galbo, Filipo; Montes, David; Iracheta, Crystal; Gamboa, Venessa L; Lopez, Daisy; Yourshaw, Michael; Lawrence, Carolyn A; Aisner, Dara L; Fitzpatrick, Carrie; McNerney, Megan E; Wang, Y Lynn; Andrade, Jorge; Volchenboum, Samuel L; Furtado, Larissa V; Ritterhouse, Lauren L; Segal, Jeremy P

    2018-04-24

    Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory, a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. The System for Informatics in the Molecular Pathology Laboratory was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of the system, its clinical validation at the Genomic and Molecular Pathology Division at the University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing. Copyright © 2018. Published by Elsevier Inc.

  20. Total and Direct Correlation Function Integrals from Molecular Simulation of Binary Systems

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; O’Connell, John P.; Peters, Günther H.J.

    2011-01-01

    The possibility for obtaining derivative properties for mixtures from integrals of spatial total and direct correlation functions obtained from molecular dynamics simulations is explored. Theoretically well-supported methods are examined to extend simulation radial distribution functions to long...... are consistent with an excess Helmholtz energy model fitted to available simulations. In addition, simulations of water/methanol and water/t-butanol mixtures have been carried out. The method yields results for partial molar volumes, activity coefficient derivatives, and individual correlation function integrals...... in reasonable agreement with smoothed experimental data. The proposed method for obtaining correlation function integrals is shown to perform at least as well as or better than two previously published approaches....