Dynamic combinatorial chemistry
Otto, Sijbren; Furlan, Ricardo L.E.; Sanders, Jeremy K.M.
2002-01-01
A combinatorial library that responds to its target by increasing the concentration of strong binders at the expense of weak binders sounds ideal. Dynamic combinatorial chemistry has the potential to achieve exactly this. In this review, we will highlight the unique features that distinguish dynamic
Dynamic Combinatorial Chemistry
DEFF Research Database (Denmark)
Lisbjerg, Micke
This thesis is divided into seven chapters, which can all be read individually. The first chapter, however, contains a general introduction to the chemistry used in the remaining six chapters, and it is therefore recommended to read chapter one before reading the other chapters. Chapter 1...... is a general introductory chapter for the whole thesis. The history and concepts of dynamic combinatorial chemistry are described, as are some of the new and intriguing results recently obtained. Finally, the properties of a broad range of hexameric macrocycles are described in detail. Chapter 2 gives...
Dynamic combinatorial libraries : new opportunities in systems chemistry
Hunt, Rosemary A. R.; Otto, Sijbren; Hunt, Rosemary A.R.
2011-01-01
Combinatorial chemistry is a tool for selecting molecules with special properties. Dynamic combinatorial chemistry started off aiming to be just that. However, unlike ordinary combinatorial chemistry, the interconnectedness of dynamic libraries gives them an extra dimension. An understanding of
Dynamic combinatorial chemistry with diselenides and disulfides in water
DEFF Research Database (Denmark)
Rasmussen, Brian; Sørensen, Anne; Gotfredsen, Henrik
2014-01-01
Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water. At neutral pH, diselenides are found to mix with disulfides and form dynamic combinatorial libraries of diselenides, disulfides, and selenenylsulfides. This journal is......Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water. At neutral pH, diselenides are found to mix with disulfides and form dynamic combinatorial libraries of diselenides, disulfides, and selenenylsulfides. This journal is...
DEFF Research Database (Denmark)
Nielsen, John
1994-01-01
An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds.......An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds....
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
National Research Council Canada - National Science Library
Low, Tammy K
2006-01-01
.... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.
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.
Angelin, Marcus; Larsson, Rikard; Vongvilai, Pornrapee; Ramstrom, Olof
2010-01-01
In this laboratory experiment, college students are introduced to dynamic combinatorial chemistry (DCC) and apply it to determine the substrate selectivity of acetylcholinesterase (AChE). Initially, the students construct a chemical library of dynamically interchanging thioesters and thiols. Then, AChE is added and allowed to select and hydrolyze…
Dynamic combinatorial chemistry at the phospholipid bilayer interface
Mansfeld, Friederike M.; Au-Yeung, Ho Yu; Sanders, Jeremy K.M.; Otto, Sijbren
2010-01-01
Background: Molecular recognition at the environment provided by the phospholipid bilayer interface plays an important role in biology and is subject of intense investigation. Dynamic combinatorial chemistry is a powerful approach for exploring molecular recognition, but has thus far not been
Dynamic Combinatorial Chemistry with Diselenides, Disulfides, Imines and Metal Coordination
DEFF Research Database (Denmark)
Sørensen, Anne
combinatorial chemistry, namely the reversible diselenide exchange reaction. The first part of the thesis describes the development of a thermally induced OAr → SeAr migration reaction. Here, it was proven possible to rearrange a variety of substituted O-aryl selenocarbamates into the corresponding Se...
International Nuclear Information System (INIS)
Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira
2004-01-01
Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
2006-08-01
organic, and biochemistry, lectured in chemistry of weapons, and researched on ionic liquids and nucleic acid derivatives. She discovered her joy of...Products from oligomerization of the dimer scaffold or olefin isomerization are excluded from these projected numbers.97,98 The number of...Figure 3-8). This is excluding any olefin isomerization products or oligomerization of the cyclic scaffold. If stereoisomers are considered, then
Drożdż, Wojciech; Kołodziejski, Michał; Markiewicz, Grzegorz; Jenczak, Anna; Stefankiewicz, Artur R
2015-07-17
We describe here the generation of new donor-acceptor disulfide architectures obtained in aqueous solution at physiological pH. The application of a dynamic combinatorial chemistry approach allowed us to generate a large number of new disulfide macrocyclic architectures together with a new type of [2]catenanes consisting of four distinct components. Up to fifteen types of structurally-distinct dynamic architectures have been generated through one-pot disulfide exchange reactions between four thiol-functionalized aqueous components. The distribution of disulfide products formed was found to be strongly dependent on the structural features of the thiol components employed. This work not only constitutes a success in the synthesis of topologically- and morphologically-complex targets, but it may also open new horizons for the use of this methodology in the construction of molecular machines.
Monjas, Leticia; Swier, Lotteke J Y M; Setyawati, Inda; Slotboom, Dirk Jan; Hirsch, Anna Katharina Herta
2017-01-01
We applied dynamic combinatorial chemistry (DCC) to identify ligands of ThiT, the S-component of the energy-coupling factor (ECF) transporter for thiamine in Lactococcus lactis. We used a pre-equilibrated dynamic combinatorial library (DCL) and saturation-transfer difference (STD) NMR spectroscopy
Frei, Priska; Pang, Lijuan; Silbermann, Marleen; Eriş, Deniz; Mühlethaler, Tobias; Schwardt, Oliver; Ernst, Beat
2017-08-25
Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
International Nuclear Information System (INIS)
Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira
2006-01-01
Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support
Mondal, Milon; Radeva, Nedyalka; Fanlo-Virgos, Hugo; Otto, Sijbren; Klebe, Gerhard; Hirsch, Anna K. H.
2016-01-01
Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for
Accessing Specific Peptide Recognition by Combinatorial Chemistry
DEFF Research Database (Denmark)
Li, Ming
Molecular recognition is at the basis of all processes for life, and plays a central role in many biological processes, such as protein folding, the structural organization of cells and organelles, signal transduction, and the immune response. Hence, my PhD project is entitled “Accessing Specific...... Peptide Recognition by Combinatorial Chemistry”. Molecular recognition is a specific interaction between two or more molecules through noncovalent bonding, such as hydrogen bonding, metal coordination, van der Waals forces, π−π, hydrophobic, or electrostatic interactions. The association involves kinetic....... Combinatorial chemistry was invented in 1980s based on observation of functional aspects of the adaptive immune system. It was employed for drug development and optimization in conjunction with high-throughput synthesis and screening. (chapter 2) Combinatorial chemistry is able to rapidly produce many thousands...
Use of combinatorial chemistry to speed drug discovery.
Rádl, S
1998-10-01
IBC's International Conference on Integrating Combinatorial Chemistry into the Discovery Pipeline was held September 14-15, 1998. The program started with a pre-conference workshop on High-Throughput Compound Characterization and Purification. The agenda of the main conference was divided into sessions of Synthesis, Automation and Unique Chemistries; Integrating Combinatorial Chemistry, Medicinal Chemistry and Screening; Combinatorial Chemistry Applications for Drug Discovery; and Information and Data Management. This meeting was an excellent opportunity to see how big pharma, biotech and service companies are addressing the current bottlenecks in combinatorial chemistry to speed drug discovery. (c) 1998 Prous Science. All rights reserved.
DNA-Encoded Dynamic Combinatorial Chemical Libraries.
Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin
2015-06-26
Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Antiparallel Dynamic Covalent Chemistries
Matysiak, Bartosz M.; Nowak, Piotr; Cvrtila, Ivica; Pappas, Charalampos G.; Liu, Bin; Komaromy, David; Otto, Sijbren
2017-01-01
The ability to design reaction networks with high, but addressable complexity is a necessary prerequisite to make advanced functional chemical systems. Dynamic combinatorial chemistry has, proven to be a useful tool in achieving complexity, however with some limitations in controlling it. Herein we
Heterogenous phase as a mean in combinatorial chemistry
International Nuclear Information System (INIS)
Abdel-Hamid, S.G.
2007-01-01
Combinatorial chemistry is a rapid and inexpensive technique for the synthesis of hundreds of thousands of organic compounds of potential medicinal activity. In the past few decades a large number of combinatorial libraries have been constructed, and significantly supplement the chemical diversity of the traditional collections of the potentially active medicinal compounds. Solid phase synthesis was used to enrich the combinatorial chemistry libraries, through the use of solid supports (resins) and their modified forms. Most of the new libraries of compounds appeared recently, were synthesized by the use of solid-phase. Solid-phase combinatorial chemistry (SPCC) is now considered as an outstanding branch in pharmaceutical chemistry research and used extensively as a tool for drug discovery within the context of high-throughput chemical synthesis. The best pure libraries synthesized by the use of solid phase combinatorial chemistry (SPCC) may well be those of intermediate complexity that are free of artifact-causing nuisance compounds. (author)
Antiparallel Dynamic Covalent Chemistries.
Matysiak, Bartosz M; Nowak, Piotr; Cvrtila, Ivica; Pappas, Charalampos G; Liu, Bin; Komáromy, Dávid; Otto, Sijbren
2017-05-17
The ability to design reaction networks with high, but addressable complexity is a necessary prerequisite to make advanced functional chemical systems. Dynamic combinatorial chemistry has proven to be a useful tool in achieving complexity, however with some limitations in controlling it. Herein we introduce the concept of antiparallel chemistries, in which the same functional group can be channeled into one of two reversible chemistries depending on a controllable parameter. Such systems allow both for achieving complexity, by combinatorial chemistry, and addressing it, by switching from one chemistry to another by controlling an external parameter. In our design the two antiparallel chemistries are thiol-disulfide exchange and thio-Michael addition, sharing the thiol as the common building block. By means of oxidation and reduction the system can be reversibly switched from predominantly thio-Michael chemistry to predominantly disulfide chemistry, as well as to any intermediate state. Both chemistries operate in water, at room temperature, and at mildly basic pH, which makes them a suitable platform for further development of systems chemistry.
Novel Combinatorial Chemistry-Derived Inhibitors of Oncogenic Phosphatases
National Research Council Canada - National Science Library
Lazo, John
1999-01-01
Our overall goal of this US Army Breast Cancer Grant entitled "Novel Combinatorial Chemistry-Derived Inhibitors of Oncogenic Phosphatases" is to identity and develop novel therapeutic agents for human breast cancer...
Mondal, Milon; Radeva, Nedyalka; Fanlo-Virgós, Hugo; Otto, Sijbren; Klebe, Gerhard; Hirsch, Anna K H
2016-08-01
Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X-ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
Mondal, Milon; Radeva, Nedyalka; Fanlo‐Virgós, Hugo; Otto, Sijbren; Klebe, Gerhard
2016-01-01
Abstract Fragment‐based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit‐identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X‐ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis‐acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240‐fold improvement in potency compared to the parent hits. Subsequent X‐ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit‐identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit‐to‐lead optimization. PMID:27400756
Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries
Directory of Open Access Journals (Sweden)
Sanna L. Diemer
2015-09-01
Full Text Available Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system.
Combinatorial chemistry approach to development of molecular plastic solar cells
Godovsky, Dmitri; Inganäs, Olle; Brabec, Christoph J.; Sariciftci, N. Serdar; Hummelen, Jan C.; Janssen, Rene A.J.; Prato, M.; Maggini, M.; Segura, Jose; Martin, Nazario
1999-01-01
We used a combinatorial chemistry approach to develop the molecular plastic solar cells based on soluble fullerene derivatives or solubilized TCNQ molecules in combination with conjugated polymers. Profiles, formed by the diffusion of low molecular weight component in the spin-cast polymer host were
Method and apparatus for combinatorial chemistry
Foote, Robert S [Oak Ridge, TN
2012-06-05
A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.
Dendrimer-based dynamic combinatorial libraries
Chang, T.; Meijer, E.W.
2005-01-01
The aim of this project is to create water-sol. dynamic combinatorial libraries based upon dendrimer-guest complexes. The guest mols. are designed to bind to dendrimers using multiple secondary interactions, such as electrostatics and hydrogen bonding. We have been able to incorporate various guest
Dynamical System Approaches to Combinatorial Optimization
DEFF Research Database (Denmark)
Starke, Jens
2013-01-01
of large times as an asymptotically stable point of the dynamics. The obtained solutions are often not globally optimal but good approximations of it. Dynamical system and neural network approaches are appropriate methods for distributed and parallel processing. Because of the parallelization......Several dynamical system approaches to combinatorial optimization problems are described and compared. These include dynamical systems derived from penalty methods; the approach of Hopfield and Tank; self-organizing maps, that is, Kohonen networks; coupled selection equations; and hybrid methods...... thereof can be used as models for many industrial problems like manufacturing planning and optimization of flexible manufacturing systems. This is illustrated for an example in distributed robotic systems....
Solid-Phase Synthesis of Small Molecule Libraries using Double Combinatorial Chemistry
DEFF Research Database (Denmark)
Nielsen, John; Jensen, Flemming R.
1997-01-01
The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can be demons......The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can...
Solid-Phase Synthesis of Small Molecule Libraries using Double Combinatorial Chemistry
DEFF Research Database (Denmark)
Nielsen, John; Jensen, Flemming R.
1997-01-01
The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can be demons...
Intrinsic information carriers in combinatorial dynamical systems
Harmer, Russ; Danos, Vincent; Feret, Jérôme; Krivine, Jean; Fontana, Walter
2010-09-01
Many proteins are composed of structural and chemical features—"sites" for short—characterized by definite interaction capabilities, such as noncovalent binding or covalent modification of other proteins. This modularity allows for varying degrees of independence, as the behavior of a site might be controlled by the state of some but not all sites of the ambient protein. Independence quickly generates a startling combinatorial complexity that shapes most biological networks, such as mammalian signaling systems, and effectively prevents their study in terms of kinetic equations—unless the complexity is radically trimmed. Yet, if combinatorial complexity is key to the system's behavior, eliminating it will prevent, not facilitate, understanding. A more adequate representation of a combinatorial system is provided by a graph-based framework of rewrite rules where each rule specifies only the information that an interaction mechanism depends on. Unlike reactions, which deal with molecular species, rules deal with patterns, i.e., multisets of molecular species. Although the stochastic dynamics induced by a collection of rules on a mixture of molecules can be simulated, it appears useful to capture the system's average or deterministic behavior by means of differential equations. However, expansion of the rules into kinetic equations at the level of molecular species is not only impractical, but conceptually indefensible. If rules describe bona fide patterns of interaction, molecular species are unlikely to constitute appropriate units of dynamics. Rather, we must seek aggregate variables reflective of the causal structure laid down by the rules. We call these variables "fragments" and the process of identifying them "fragmentation." Ideally, fragments are aspects of the system's microscopic population that the set of rules can actually distinguish on average; in practice, it may only be feasible to identify an approximation to this. Most importantly, fragments are
Intrinsic information carriers in combinatorial dynamical systems.
Harmer, Russ; Danos, Vincent; Feret, Jérôme; Krivine, Jean; Fontana, Walter
2010-09-01
Many proteins are composed of structural and chemical features--"sites" for short--characterized by definite interaction capabilities, such as noncovalent binding or covalent modification of other proteins. This modularity allows for varying degrees of independence, as the behavior of a site might be controlled by the state of some but not all sites of the ambient protein. Independence quickly generates a startling combinatorial complexity that shapes most biological networks, such as mammalian signaling systems, and effectively prevents their study in terms of kinetic equations-unless the complexity is radically trimmed. Yet, if combinatorial complexity is key to the system's behavior, eliminating it will prevent, not facilitate, understanding. A more adequate representation of a combinatorial system is provided by a graph-based framework of rewrite rules where each rule specifies only the information that an interaction mechanism depends on. Unlike reactions, which deal with molecular species, rules deal with patterns, i.e., multisets of molecular species. Although the stochastic dynamics induced by a collection of rules on a mixture of molecules can be simulated, it appears useful to capture the system's average or deterministic behavior by means of differential equations. However, expansion of the rules into kinetic equations at the level of molecular species is not only impractical, but conceptually indefensible. If rules describe bona fide patterns of interaction, molecular species are unlikely to constitute appropriate units of dynamics. Rather, we must seek aggregate variables reflective of the causal structure laid down by the rules. We call these variables "fragments" and the process of identifying them "fragmentation." Ideally, fragments are aspects of the system's microscopic population that the set of rules can actually distinguish on average; in practice, it may only be feasible to identify an approximation to this. Most importantly, fragments are
Combinatorial Micro-Macro Dynamical Systems
Diaz, Rafael; Villamarin, Sergio
2015-01-01
The second law of thermodynamics states that the entropy of an isolated system is almost always increasing. We propose combinatorial formalizations of the second law and explore their conditions of possibilities.
Combinatorial computational chemistry approach to the design of metal catalysts for deNOx
International Nuclear Information System (INIS)
Endou, Akira; Jung, Changho; Kusagaya, Tomonori; Kubo, Momoji; Selvam, Parasuraman; Miyamoto, Akira
2004-01-01
Combinatorial chemistry is an efficient technique for the synthesis and screening of a large number of compounds. Recently, we introduced the combinatorial approach to computational chemistry for catalyst design and proposed a new method called ''combinatorial computational chemistry''. In the present study, we have applied this combinatorial computational chemistry approach to the design of precious metal catalysts for deNO x . As the first step of the screening of the metal catalysts, we studied Rh, Pd, Ag, Ir, Pt, and Au clusters regarding the adsorption properties towards NO molecule. It was demonstrated that the energetically most stable adsorption state of NO on Ir model cluster, which was irrespective of both the shape and number of atoms including the model clusters
cDREM: inferring dynamic combinatorial gene regulation.
Wise, Aaron; Bar-Joseph, Ziv
2015-04-01
Genes are often combinatorially regulated by multiple transcription factors (TFs). Such combinatorial regulation plays an important role in development and facilitates the ability of cells to respond to different stresses. While a number of approaches have utilized sequence and ChIP-based datasets to study combinational regulation, these have often ignored the combinational logic and the dynamics associated with such regulation. Here we present cDREM, a new method for reconstructing dynamic models of combinatorial regulation. cDREM integrates time series gene expression data with (static) protein interaction data. The method is based on a hidden Markov model and utilizes the sparse group Lasso to identify small subsets of combinatorially active TFs, their time of activation, and the logical function they implement. We tested cDREM on yeast and human data sets. Using yeast we show that the predicted combinatorial sets agree with other high throughput genomic datasets and improve upon prior methods developed to infer combinatorial regulation. Applying cDREM to study human response to flu, we were able to identify several combinatorial TF sets, some of which were known to regulate immune response while others represent novel combinations of important TFs.
Photoelectrochemical Hydrogen Production Using New Combinatorial Chemistry Derived Materials
Energy Technology Data Exchange (ETDEWEB)
Jaramillo, Thomas F.; Baeck, Sung-Hyeon; Kleiman-Shwarsctein, Alan; Stucky, Galen D. (PI); McFarland, Eric W. (PI)
2004-10-25
Solar photoelectrochemical water-splitting has long been viewed as one of the “holy grails” of chemistry because of its potential impact as a clean, renewable method of fuel production. Several known photocatalytic semiconductors can be used; however, the fundamental mechanisms of the process remain poorly understood and no known material has the required properties for cost effective hydrogen production. In order to investigate morphological and compositional variations in metal oxides as they relate to opto-electrochemical properties, we have employed a combinatorial methodology using automated, high-throughput, electrochemical synthesis and screening together with conventional solid-state methods. This report discusses a number of novel, high-throughput instruments developed during this project for the expeditious discovery of improved materials for photoelectrochemical hydrogen production. Also described within this report are results from a variety of materials (primarily tungsten oxide, zinc oxide, molybdenum oxide, copper oxide and titanium dioxide) whose properties were modified and improved by either layering, inter-mixing, or doping with one or more transition metals. Furthermore, the morphologies of certain materials were also modified through the use of structure directing agents (SDA) during synthesis to create mesostructures (features 2-50 nm) that increased surface area and improved rates of hydrogen production.
Peptide mimic for influenza vaccination using nonnatural combinatorial chemistry
Miles, John J.; Tan, Mai Ping; Dolton, Garry; Galloway, Sarah A.E.; Laugel, Bruno; Makinde, Julia; Matthews, Katherine K.; Watkins, Thomas S.; Wong, Yide; Clark, Richard J.; Pentier, Johanne M.; Attaf, Meriem; Lissina, Anya; Ager, Ann; Gallimore, Awen; Gras, Stephanie; Rossjohn, Jamie; Burrows, Scott R.; Cole, David K.; Price, David A.
2018-01-01
Polypeptide vaccines effectively activate human T cells but suffer from poor biological stability, which confines both transport logistics and in vivo therapeutic activity. Synthetic biology has the potential to address these limitations through the generation of highly stable antigenic “mimics” using subunits that do not exist in the natural world. We developed a platform based on D–amino acid combinatorial chemistry and used this platform to reverse engineer a fully artificial CD8+ T cell agonist that mirrored the immunogenicity profile of a native epitope blueprint from influenza virus. This nonnatural peptide was highly stable in human serum and gastric acid, reflecting an intrinsic resistance to physical and enzymatic degradation. In vitro, the synthetic agonist stimulated and expanded an archetypal repertoire of polyfunctional human influenza virus–specific CD8+ T cells. In vivo, specific responses were elicited in naive humanized mice by subcutaneous vaccination, conferring protection from subsequent lethal influenza challenge. Moreover, the synthetic agonist was immunogenic after oral administration. This proof-of-concept study highlights the power of synthetic biology to expand the horizons of vaccine design and therapeutic delivery. PMID:29528337
Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes
Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes
2007-01-01
This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the
DEFF Research Database (Denmark)
Tong, Glenn; Nielsen, John
1996-01-01
The actinomycin antibiotics bind to nucleic acids via both intercalation and hydrogen bonding. We found this 'double-action attack' mechanism very attractive in our search for a novel class of nucleic acid binders. A highly convergent, solid-phase synthetic strategy has been developed for a class...... with the requirements for combinatorial synthesis and furthermore, the final segment condensation allows, for the first time, double-combinatorial chemistry to be performed where two combinatorial libraries can be reacted with each other. Copyright (C) 1996 Elsevier Science Ltd....
Combinatorial chemistry on solid support in the search for central nervous system agents.
Zajdel, Paweł; Pawłowski, Maciej; Martinez, Jean; Subra, Gilles
2009-08-01
The advent of combinatorial chemistry was one of the most important developments, that has significantly contributed to the drug discovery process. Within just a few years, its initial concept aimed at production of libraries containing huge number of compounds (thousands to millions), so called screening libraries, has shifted towards preparation of small and medium-sized rationally designed libraries. When applicable, the use of solid supports for the generation of libraries has been a real breakthrough in enhancing productivity. With a limited amount of resin and simple manual workups, the split/mix procedure may generate thousands of bead-tethered compounds. Beads can be chemically or physically encoded to facilitate the identification of a hit after the biological assay. Compartmentalization of solid supports using small reactors like teabags, kans or pellicular discrete supports like Lanterns resulted in powerful sort and combine technologies, relying on codes 'written' on the reactor, and thus reducing the need for automation and improving the number of compounds synthesized. These methods of solid-phase combinatorial chemistry have been recently supported by introduction of solid-supported reagents and scavenger resins. The first part of this review discusses the general premises of combinatorial chemistry and some methods used in the design of primary and focused combinatorial libraries. The aim of the second part is to present combinatorial chemistry methodologies aimed at discovering bioactive compounds acting on diverse GPCR involved in central nervous system disorders.
Isocyanide based multi component reactions in combinatorial chemistry.
Dömling, A.
1998-01-01
Although usually regarded as a recent development, the combinatorial approach to the synthesis of libraries of new drug candidates was first described as early as 1961 using the isocyanide-based one-pot multicomponent Ugi reaction. Isocyanide-based multi component reactions (MCR's) markedly differ
Burello, E.; Bologa, C.; Frecer, V.; Miertus, S.
Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anticancer drugs. These illustrate library focusing strategies.
Potyrailo, Radislav A; Chisholm, Bret J; Morris, William G; Cawse, James N; Flanagan, William P; Hassib, Lamyaa; Molaison, Chris A; Ezbiansky, Karin; Medford, George; Reitz, Hariklia
2003-01-01
Coupling of combinatorial chemistry methods with high-throughput (HT) performance testing and measurements of resulting properties has provided a powerful set of tools for the 10-fold accelerated discovery of new high-performance coating materials for automotive applications. Our approach replaces labor-intensive steps with automated systems for evaluation of adhesion of 8 x 6 arrays of coating elements that are discretely deposited on a single 9 x 12 cm plastic substrate. Performance of coatings is evaluated with respect to their resistance to adhesion loss, because this parameter is one of the primary considerations in end-use automotive applications. Our HT adhesion evaluation provides previously unavailable capabilities of high speed and reproducibility of testing by using a robotic automation, an expanded range of types of tested coatings by using the coating tagging strategy, and an improved quantitation by using high signal-to-noise automatic imaging. Upon testing, the coatings undergo changes that are impossible to quantitatively predict using existing knowledge. Using our HT methodology, we have developed several coatings leads. These HT screening results for the best coating compositions have been validated on the traditional scales of coating formulation and adhesion loss testing. These validation results have confirmed the superb performance of combinatorially developed coatings over conventional coatings on the traditional scale.
DNA functionalization by dynamic chemistry
Directory of Open Access Journals (Sweden)
Zeynep Kanlidere
2016-10-01
Full Text Available Dynamic combinatorial chemistry (DCC is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80% was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.
Energy Technology Data Exchange (ETDEWEB)
Weber, Stephen G. [University of Pittsburgh, Pittsburgh, Pennsylvania
1998-08-22
The power of combinatorial chemistry and related high throughput synthetic strategies is currently being pursued as a fruitful way to develop molecules and materials with new properties. The strategy is motivated, for example in the pharmaceutical industry, by the difficulty of designing molecules to bind to specific sites on target biomolecules. By synthesizing a variety of similar structures, and then finding the one that has the most potent activity, new so-called lead structures will be found rapidly. Existing lead structures can be optimized. This relatively new approach has many implications for separation science. The most obvious is the call for more separations power: higher resolution, lower concentrations, higher speed. This pressure butresses the traditional directions of research into the development of more useful separations. The advent of chip-based, electroosmotically pumped systems1 will certainly accelerate progress in this traditional direction. The progress in combinatorial chemistry and related synthetic strategies gives rise to two other, broadly significant possibilities for large changes in separation science. One possibility results from the unique requirements of the synthesis of a huge number of products simultaneously. Can syntheses and separations be designed to work together to create strategies that lead to mixtures containing only desired products but without side products? The other possibility results from the need for molecular selectivity in separations. Can combinatorial syntheses and related strategies be used in the development of better separations media? A workshop in two parts was held. In one half-day session, pedagogical presentations educated across the barriers of discipline and scale. In the second half-day session, the participants broke into small groups to flesh out new ideas. A panel summarized the breakout discussions.
Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.
Lehn, Jean-Marie
2012-01-01
Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.
Selective host molecules obtained by dynamic adaptive chemistry.
Matache, Mihaela; Bogdan, Elena; Hădade, Niculina D
2014-02-17
Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis-optimization process. The second was the use of a "brutal force" approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, "rational design" often resulted in time-consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. "Combinatorial chemistry" suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Therrien, Eric; Englebienne, Pablo; Arrowsmith, Andrew G; Mendoza-Sanchez, Rodrigo; Corbeil, Christopher R; Weill, Nathanael; Campagna-Slater, Valérie; Moitessier, Nicolas
2012-01-23
As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.
Boehm, Markus; Wu, Tong-Ying; Claussen, Holger; Lemmen, Christian
2008-04-24
Large collections of combinatorial libraries are an integral element in today's pharmaceutical industry. It is of great interest to perform similarity searches against all virtual compounds that are synthetically accessible by any such library. Here we describe the successful application of a new software tool CoLibri on 358 combinatorial libraries based on validated reaction protocols to create a single chemistry space containing over 10 (12) possible products. Similarity searching with FTrees-FS allows the systematic exploration of this space without the need to enumerate all product structures. The search result is a set of virtual hits which are synthetically accessible by one or more of the existing reaction protocols. Grouping these virtual hits by their synthetic protocols allows the rapid design and synthesis of multiple follow-up libraries. Such library ideas support hit-to-lead design efforts for tasks like follow-up from high-throughput screening hits or scaffold hopping from one hit to another attractive series.
International Nuclear Information System (INIS)
Kurth, M.J.; Miller, R.B.; Sawan, S.; Smith, B.F.
1998-01-01
'(1) Develop rapid discovery and optimization approaches to new water-soluble chelating polymers for use in Polymer Filtration (PF) systems, and (2) evaluate the concept of using water and organic soluble polymers as new solid supports for combinatorial synthesis. Polymer Filtration (PF), which uses water-soluble metal-binding polymers to sequester metal ions in dilute solution with ultrafiltration (UF) to separate the polymers, is a new technology to selectively remove or recover hazardous and valuable metal ions. Future directions in PF must include rapid development, testing, and characterization of new metal-binding polymers. Thus, the authors are building upon and adapting the combinatorial chemistry approach developed for rapid molecule generation for the drug industry to the rapid development of new chelating polymers. The authors have focused on four areas including the development of: (1) synthetic procedures, (2) small ultrafiltration equipment compatible with organic- and aqueous-based combinatorial synthesis, (3) rapid assay techniques, and (4) polymer characterization techniques.'
Jiménez-Moreno, Ester; Gómez, Ana M; Bastida, Agatha; Corzana, Francisco; Jiménez-Oses, Gonzalo; Jiménez-Barbero, Jesús; Asensio, Juan Luis
2015-03-27
Electrostatic and charge-transfer contributions to CH-π complexes can be modulated by attaching electron-withdrawing substituents to the carbon atom. While clearly stabilizing in the gas phase, the outcome of this chemical modification in water is more difficult to predict. Herein we provide a definitive and quantitative answer to this question employing a simple strategy based on dynamic combinatorial chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Dibó, Gábor
2012-02-01
Combinatorial chemistry was introduced in the 1980s. It provided the possibility to produce new compounds in practically unlimited number. New strategies and technologies have also been developed that made it possible to screen very large number of compounds and to identify useful components in mixtures containing millions of different substances. This dramatically changed the drug discovery process and the way of thinking of synthetic chemists. In addition, combinatorial strategies became useful in areas such as pharmaceutical research, agrochemistry, catalyst design, and materials research. Prof. Árpád Furka is one of the pioneers of combinatorial chemistry.
Brady, John T.; Warner, Benjamin P.; Bridgewater, Jon S.; Havrilla, George J.; Morris, David E.; Buscher, C. Thomas
2000-07-01
We are currently investigating the potential chemistry of the 3013 Standard waste storage containers. These containers are filled with waste that is a mixture of inorganic salts and plutonium oxide that has been calcined to remove water and other volatiles. There has been concern about possible pressure buildup due to the formation of hydrogen or other gases. We are utilizing a combinatorial chemistry approach to investigate a range of possible reactions that may occur in the containers with various concentrations of metal oxides and inorganic salts.
A combinatorial framework to quantify peak/pit asymmetries in complex dynamics
Hasson, Uri; Iacovacci, Jacopo; Davis, Ben; Flanagan, Ryan; Tagliazucchi, E.; Laufs, Helmut; Lacasa, Lucas
2018-01-01
We explore a combinatorial framework which efficiently quantifies the asymmetries between minima and maxima in local fluctuations of time series. We first showcase its performance by applying it to a battery of synthetic cases. We find rigorous results on some canonical dynamical models (stochastic
Roberts, Sarah L.; Furlan, Ricardo L.E.; Otto, Sijbren; Sanders, Jeremy K.M.
2003-01-01
Three building blocks of general structure (MeO)2CH–aromatic linker–Pro–amino acid–NHNH2 have been prepared and tested in acid-catalysed dynamic combinatorial libraries. Exposure of these libraries to LiI and NaI led to the amplification of three macrocyclic pseudopeptide receptors. The receptors
International Nuclear Information System (INIS)
Fujimoto, K.; Takahashi, H.; Ito, S.; Inoue, S.; Watanabe, M.
2006-01-01
As a tool to facilitate future material explorations, our group has developed a new combinatorial system for the high-throughput preparation of compounds made up of more than three components. The system works in two steps: the atomization of a liquid by a high electric field followed by deposition to a grounded substrate. The combinatorial system based on this method has plural syringe pumps. The each starting materials are fed through the syringe pumps into a manifold, thoroughly mixed as they pass through the manifold, and atomized from the tip of a stainless steel nozzle onto a grounded substrate
Besenius, Pol; Cormack, Peter A.G.; Liu, Jingyuan; Otto, Sijbren; Sanders, Jeremy K.M.; Sherrington, David C.
2008-01-01
The thermodynamically controlled synthesis and isolation of macrocyclic receptors from dynamic combinatorial libraries has been achieved in a single step using a polymer-supported template. The templates were cinchona alkaloids which show interesting enantio- and diastereoselective molecular
Combinatorial-topological framework for the analysis of global dynamics
Bush, Justin; Gameiro, Marcio; Harker, Shaun; Kokubu, Hiroshi; Mischaikow, Konstantin; Obayashi, Ippei; Pilarczyk, Paweł
2012-12-01
We discuss an algorithmic framework based on efficient graph algorithms and algebraic-topological computational tools. The framework is aimed at automatic computation of a database of global dynamics of a given m-parameter semidynamical system with discrete time on a bounded subset of the n-dimensional phase space. We introduce the mathematical background, which is based upon Conley's topological approach to dynamics, describe the algorithms for the analysis of the dynamics using rectangular grids both in phase space and parameter space, and show two sample applications.
Combinatorial-topological framework for the analysis of global dynamics.
Bush, Justin; Gameiro, Marcio; Harker, Shaun; Kokubu, Hiroshi; Mischaikow, Konstantin; Obayashi, Ippei; Pilarczyk, Paweł
2012-12-01
We discuss an algorithmic framework based on efficient graph algorithms and algebraic-topological computational tools. The framework is aimed at automatic computation of a database of global dynamics of a given m-parameter semidynamical system with discrete time on a bounded subset of the n-dimensional phase space. We introduce the mathematical background, which is based upon Conley's topological approach to dynamics, describe the algorithms for the analysis of the dynamics using rectangular grids both in phase space and parameter space, and show two sample applications.
International Nuclear Information System (INIS)
Schnabel, Volker; Köhler, Mathias; Evertz, Simon; Gamcova, Jana; Bednarcik, Jozef; Music, Denis; Raabe, Dierk; Schneider, Jochen M.
2016-01-01
An efficient way to study the relationship between chemical composition and mechanical properties of thin films is to utilize the combinatorial approach, where spatially resolved mechanical property measurements are conducted along a concentration gradient. However, for thin film glasses many properties including the mechanical response are affected by chemical topology. Here a novel method is introduced which enables spatially resolved short range order analysis along concentration gradients of combinatorially synthesized metallic glass thin films. For this purpose a CoZrTaB metallic glass film of 3 μm thickness is deposited on a polyimide foil, which is investigated by high energy X-ray diffraction in transmission mode. Through the correlative chemistry-topology-stiffness investigation, we observe that an increase in metalloid concentration from 26.4 to 32.7 at% and the associated formation of localized (hybridized) metal – metalloid bonds induce a 10% increase in stiffness. Concomitantly, along the same composition gradient, a metalloid-concentration-induced increase in first order metal - metal bond distances of 1% is observed, which infers itinerant (metallic) bond weakening. Hence, the metalloid concentration induced increase in hybridized bonding dominates the corresponding weakening of metallic bonds.
Chang, Yuchao; Tang, Hongying; Cheng, Yongbo; Zhao, Qin; Yuan, Baoqing Li andXiaobing
2017-07-19
Routing protocols based on topology control are significantly important for improving network longevity in wireless sensor networks (WSNs). Traditionally, some WSN routing protocols distribute uneven network traffic load to sensor nodes, which is not optimal for improving network longevity. Differently to conventional WSN routing protocols, we propose a dynamic hierarchical protocol based on combinatorial optimization (DHCO) to balance energy consumption of sensor nodes and to improve WSN longevity. For each sensor node, the DHCO algorithm obtains the optimal route by establishing a feasible routing set instead of selecting the cluster head or the next hop node. The process of obtaining the optimal route can be formulated as a combinatorial optimization problem. Specifically, the DHCO algorithm is carried out by the following procedures. It employs a hierarchy-based connection mechanism to construct a hierarchical network structure in which each sensor node is assigned to a special hierarchical subset; it utilizes the combinatorial optimization theory to establish the feasible routing set for each sensor node, and takes advantage of the maximum-minimum criterion to obtain their optimal routes to the base station. Various results of simulation experiments show effectiveness and superiority of the DHCO algorithm in comparison with state-of-the-art WSN routing algorithms, including low-energy adaptive clustering hierarchy (LEACH), hybrid energy-efficient distributed clustering (HEED), genetic protocol-based self-organizing network clustering (GASONeC), and double cost function-based routing (DCFR) algorithms.
Bagheri, Neda; Shiina, Marisa; Lauffenburger, Douglas A; Korn, W Michael
2011-02-01
Oncolytic adenoviruses, such as ONYX-015, have been tested in clinical trials for currently untreatable tumors, but have yet to demonstrate adequate therapeutic efficacy. The extent to which viruses infect targeted cells determines the efficacy of this approach but many tumors down-regulate the Coxsackievirus and Adenovirus Receptor (CAR), rendering them less susceptible to infection. Disrupting MAPK pathway signaling by pharmacological inhibition of MEK up-regulates CAR expression, offering possible enhanced adenovirus infection. MEK inhibition, however, interferes with adenovirus replication due to resulting G1-phase cell cycle arrest. Therefore, enhanced efficacy will depend on treatment protocols that productively balance these competing effects. Predictive understanding of how to attain and enhance therapeutic efficacy of combinatorial treatment is difficult since the effects of MEK inhibitors, in conjunction with adenovirus/cell interactions, are complex nonlinear dynamic processes. We investigated combinatorial treatment strategies using a mathematical model that predicts the impact of MEK inhibition on tumor cell proliferation, ONYX-015 infection, and oncolysis. Specifically, we fit a nonlinear differential equation system to dedicated experimental data and analyzed the resulting simulations for favorable treatment strategies. Simulations predicted enhanced combinatorial therapy when both treatments were applied simultaneously; we successfully validated these predictions in an ensuing explicit test study. Further analysis revealed that a CAR-independent mechanism may be responsible for amplified virus production and cell death. We conclude that integrated computational and experimental analysis of combinatorial therapy provides a useful means to identify treatment/infection protocols that yield clinically significant oncolysis. Enhanced oncolytic therapy has the potential to dramatically improve non-surgical cancer treatment, especially in locally advanced
Dynamics of forest soil chemistry
Energy Technology Data Exchange (ETDEWEB)
Alveteg, M
1998-11-01
Acidification caused by emissions of nitrogen and sulphur and associated adverse effects on forest ecosystems has been an issue on the political agenda for decades. Temporal aspects of soil acidification and/or recovery can be investigated using the soil chemistry model SAFE, a dynamic version of the steady-state model PROFILE used in critical loads assessment on the national level, e.g. for Sweden. In this thesis, possibilities to replace the use of apparent gibbsite solubility coefficients with a more mechanistic Al sub-model are investigated and a reconstruction model, MAKEDEP, is presented which makes hindcasts and forecasts of atmospheric deposition and nutrient uptake and cycling. A regional application of SAFE/MAKEDEP based on 622 sites in Switzerland is also presented. It is concluded that the quantitative information on pools and fluxes of Al in forest ecosystems is very limited and that there currently exists no mechanistic alternative in modelling soil solution Al. MAKEDEP is a valuable and operational tool for deriving input to dynamic soil chemistry models such as SMART, MAGIC and SAFE. For multi-layer models, e.g. the SAFE model, including nutrient cycling in MAKEDEP is shown to be important. The strength of the regional assessment strategy presented in this thesis lies in its transparency and modularity. All sub-modules, including models, transfer functions, assumptions in the data acquisition strategy, etc., can be checked and replaced individually. As the presented assessment strategy is based on knowledge and data from a wide range of scientists and fields it is of vital importance that the research community challenge the assumptions made. The many measurable intermediate results produced by the included models will hopefully encourage scientists to challenge the models through additional measurements at the calculation sites. It is concluded that current reduction plans are not sufficient for all forest ecosystems in Switzerland to recover from
International Nuclear Information System (INIS)
Smith, B.F.
1997-01-01
'The first objective of this research is to develop rapid discovery and optimization approaches to new water-soluble chelating polymers. A byproduct of the development approach will be the new, selective, and efficient metal-binding agents. The second objective is to evaluate the concept of using water and organic soluble polymers as new solid supports for combinatorial synthesis. The technology under development, Polymer Filtration (PF), is a technique to selectively remove or recover hazardous and valuable metal ions and radionuclides from various dilute aqueous streams. Not only can this technology be used to remediate contaminated soils and solid surfaces and treat aqueous wastes, it can also be incorporated into facilities as a pollution prevention and waste minimization technology. Polymer Filtration uses water-soluble metal-binding polymers to sequester metal ions in dilute solution. The water-soluble polymers have a sufficiently large molecular size that they can be separated and concentrated using commercial ultrafiltration technology. Water, small organic molecules, and unbound metals pass freely through the ultrafiltration membrane while concentrating the metal-binding polymer. The polymers can then be reused by changing the solution conditions to release the metal ions. The metal-ions are recovered in concentrated form for recycle or disposal using a diafiltration process. The water-soluble polymer can be recycled for further aqueous-stream processing. To advance Polymer Filtration technology to the selectivity levels required for DOE needs. fixture directions in Polymer Filtration must include rapid development, testing, and characterization of new metal-binding polymers. The development of new chelating molecules can be equated to the process of new drugs or new materials discovery. Thus, the authors want to build upon and adapt the combinatorial chemistry approaches developed for rapid molecule generation for the drug industry to the rapid
Exact combinatorial reliability analysis of dynamic systems with sequence-dependent failures
International Nuclear Information System (INIS)
Xing Liudong; Shrestha, Akhilesh; Dai Yuanshun
2011-01-01
Many real-life fault-tolerant systems are subjected to sequence-dependent failure behavior, in which the order in which the fault events occur is important to the system reliability. Such systems can be modeled by dynamic fault trees (DFT) with priority-AND (pAND) gates. Existing approaches for the reliability analysis of systems subjected to sequence-dependent failures are typically state-space-based, simulation-based or inclusion-exclusion-based methods. Those methods either suffer from the state-space explosion problem or require long computation time especially when results with high degree of accuracy are desired. In this paper, an analytical method based on sequential binary decision diagrams is proposed. The proposed approach can analyze the exact reliability of non-repairable dynamic systems subjected to the sequence-dependent failure behavior. Also, the proposed approach is combinatorial and is applicable for analyzing systems with any arbitrary component time-to-failure distributions. The application and advantages of the proposed approach are illustrated through analysis of several examples. - Highlights: → We analyze the sequence-dependent failure behavior using combinatorial models. → The method has no limitation on the type of time-to-failure distributions. → The method is analytical and based on sequential binary decision diagrams (SBDD). → The method is computationally more efficient than existing methods.
Dynamic combinatorial and protein-templated click chemistry in medicinal chemistry
Mondal, Milon
2016-01-01
We have highlighted throughout this thesis that fragment-based drug design (FBDD) and structure-based drug design (SBDD) still constitute a number of challenges such as the risk associated with de novo SBDD and are time-consuming as they involve synthesis and validation of the binding mode of each
Kim, Joong-Hyun; Kang, Min Sil; Eltohamy, Mohamed; Kim, Tae-Hyun; Kim, Hae-Won
2016-01-01
Complete reconstruction of damaged periodontal pockets, particularly regeneration of periodontal ligament (PDL) has been a significant challenge in dentistry. Tissue engineering approach utilizing PDL stem cells and scaffolding matrices offers great opportunity to this, and applying physical and mechanical cues mimicking native tissue conditions are of special importance. Here we approach to regenerate periodontal tissues by engineering PDL cells supported on a nanofibrous scaffold under a mechanical-stressed condition. PDL stem cells isolated from rats were seeded on an electrospun polycaprolactone/gelatin directionally-oriented nanofiber membrane and dynamic mechanical stress was applied to the cell/nanofiber construct, providing nanotopological and mechanical combined cues. Cells recognized the nanofiber orientation, aligning in parallel, and the mechanical stress increased the cell alignment. Importantly, the cells cultured on the oriented nanofiber combined with the mechanical stress produced significantly stimulated PDL specific markers, including periostin and tenascin with simultaneous down-regulation of osteogenesis, demonstrating the roles of topological and mechanical cues in altering phenotypic change in PDL cells. Tissue compatibility of the tissue-engineered constructs was confirmed in rat subcutaneous sites. Furthermore, in vivo regeneration of PDL and alveolar bone tissues was examined under the rat premaxillary periodontal defect models. The cell/nanofiber constructs engineered under mechanical stress showed sound integration into tissue defects and the regenerated bone volume and area were significantly improved. This study provides an effective tissue engineering approach for periodontal regeneration-culturing PDL stem cells with combinatory cues of oriented nanotopology and dynamic mechanical stretch.
DEFF Research Database (Denmark)
Larsen, Jesper Abildgaard; Wisniewski, Rafal; Grunnet, Jacob Deleuran
2008-01-01
indicates for a given face the future simplex. In the suggested definition we allow nondeterminacy in form of splitting and merging of solution trajectories. The combinatorial vector field gives rise to combinatorial counterparts of most concepts from dynamical systems, such as duals to vector fields, flow......, flow lines, fixed points and Lyapunov functions. Finally it will be shown how this theory extends to switched dynamical systems and an algorithmic overview of how to do supervisory control will be shown towards the end....
Görlach, E; Richmond, R; Lewis, I
1998-08-01
For the last two years, the mass spectroscopy section of the Novartis Pharma Research Core Technology group has analyzed tens of thousands of multiple parallel synthesis samples from the Novartis Pharma Combinatorial Chemistry program, using an in-house developed automated high-throughput flow injection analysis electrospray ionization mass spectroscopy system. The electrospray spectra of these samples reflect the many structures present after the cleavage step from the solid support. The overall success of the sequential synthesis is mirrored in the purity of the expected end product, but the partial success of individual synthesis steps is evident in the impurities in the mass spectrum. However this latter reaction information, which is of considerable utility to the combinatorial chemist, is effectively hidden from view by the very large number of analyzed samples. This information is now revealed at the workbench of the combinatorial chemist by a novel three-dimensional display of each rack's complete mass spectral ion current using the in-house RackViewer Visual Basic application. Colorization of "forbidden loss" and "forbidden gas-adduct" zones, normalization to expected monoisotopic molecular weight, colorization of ionization intensity, and sorting by row or column were used in combination to highlight systematic patterns in the mass spectroscopy data.
Extensions of Dynamic Programming: Decision Trees, Combinatorial Optimization, and Data Mining
Hussain, Shahid
2016-01-01
This thesis is devoted to the development of extensions of dynamic programming to the study of decision trees. The considered extensions allow us to make multi-stage optimization of decision trees relative to a sequence of cost functions, to count the number of optimal trees, and to study relationships: cost vs cost and cost vs uncertainty for decision trees by construction of the set of Pareto-optimal points for the corresponding bi-criteria optimization problem. The applications include study of totally optimal (simultaneously optimal relative to a number of cost functions) decision trees for Boolean functions, improvement of bounds on complexity of decision trees for diagnosis of circuits, study of time and memory trade-off for corner point detection, study of decision rules derived from decision trees, creation of new procedure (multi-pruning) for construction of classifiers, and comparison of heuristics for decision tree construction. Part of these extensions (multi-stage optimization) was generalized to well-known combinatorial optimization problems: matrix chain multiplication, binary search trees, global sequence alignment, and optimal paths in directed graphs.
Extensions of Dynamic Programming: Decision Trees, Combinatorial Optimization, and Data Mining
Hussain, Shahid
2016-07-10
This thesis is devoted to the development of extensions of dynamic programming to the study of decision trees. The considered extensions allow us to make multi-stage optimization of decision trees relative to a sequence of cost functions, to count the number of optimal trees, and to study relationships: cost vs cost and cost vs uncertainty for decision trees by construction of the set of Pareto-optimal points for the corresponding bi-criteria optimization problem. The applications include study of totally optimal (simultaneously optimal relative to a number of cost functions) decision trees for Boolean functions, improvement of bounds on complexity of decision trees for diagnosis of circuits, study of time and memory trade-off for corner point detection, study of decision rules derived from decision trees, creation of new procedure (multi-pruning) for construction of classifiers, and comparison of heuristics for decision tree construction. Part of these extensions (multi-stage optimization) was generalized to well-known combinatorial optimization problems: matrix chain multiplication, binary search trees, global sequence alignment, and optimal paths in directed graphs.
Chemistry of carbon in dynamic sodium
International Nuclear Information System (INIS)
Lievens, F.; Casteels, F.
1980-01-01
The chemistry of carbon in sodium is described by its chemical activity measurements using alloy monitor foils, by its behaviour in the heat exchanger of the Na 2 sodium loop after 60,000 hours of operation, and by measurements with on-line meters. Efforts toward the identification of the carbon chemical states present in dynamic sodium, and responsible for the carbon chemical activity, are described. (author)
Chemistry of carbon in dynamic sodium
Energy Technology Data Exchange (ETDEWEB)
Lievens, F; Casteels, F [SCK/CEN, Mol (Belgium)
1980-05-01
The chemistry of carbon in sodium is described by its chemical activity measurements using alloy monitor foils, by its behaviour in the heat exchanger of the Na 2 sodium loop after 60,000 hours of operation, and by measurements with on-line meters. Efforts toward the identification of the carbon chemical states present in dynamic sodium, and responsible for the carbon chemical activity, are described. (author)
Controlling Chemistry in Dynamic Nanoscale Systems
DEFF Research Database (Denmark)
Jesorka, Aldo; Lizana, Ludvig; Konkoli, Zoran
2011-01-01
Spatial organization and shape dynamics are inherent properties of biological cells and cell interiors. There are strong indications that these features are important for the in vivo control of reaction parameters in biochemical transformations. Nanofluidic model devices founded on surfactant...... of the concept. Controlled release of chol-DNA molecules from SU-8 surfaces gives the possibility to dynamically change surface and/or solution properties in micro and nanoreactor applications, opening access to stable 2D chemistry on surface-based devices with potential for easy interfacing with conventional...
Molecular dynamics for irradiation driven chemistry
DEFF Research Database (Denmark)
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-01-01
A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...
Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo
2014-11-01
Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.
Directory of Open Access Journals (Sweden)
Delphine Paolantoni
2015-02-01
Full Text Available DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.
Combinatorial Nano-Bio Interfaces.
Cai, Pingqiang; Zhang, Xiaoqian; Wang, Ming; Wu, Yun-Long; Chen, Xiaodong
2018-06-08
Nano-bio interfaces are emerging from the convergence of engineered nanomaterials and biological entities. Despite rapid growth, clinical translation of biomedical nanomaterials is heavily compromised by the lack of comprehensive understanding of biophysicochemical interactions at nano-bio interfaces. In the past decade, a few investigations have adopted a combinatorial approach toward decoding nano-bio interfaces. Combinatorial nano-bio interfaces comprise the design of nanocombinatorial libraries and high-throughput bioevaluation. In this Perspective, we address challenges in combinatorial nano-bio interfaces and call for multiparametric nanocombinatorics (composition, morphology, mechanics, surface chemistry), multiscale bioevaluation (biomolecules, organelles, cells, tissues/organs), and the recruitment of computational modeling and artificial intelligence. Leveraging combinatorial nano-bio interfaces will shed light on precision nanomedicine and its potential applications.
Toward Chemical Implementation of Encoded Combinatorial Libraries
DEFF Research Database (Denmark)
Nielsen, John; Janda, Kim D.
1994-01-01
The recent application of "combinatorial libraries" to supplement existing drug screening processes might simplify and accelerate the search for new lead compounds or drugs. Recently, a scheme for encoded combinatorial chemistry was put forward to surmount a number of the limitations possessed...
International Nuclear Information System (INIS)
Zeon, Il Woon; Park, Hee Dong; Sohn, Kee Sun; Ryu, Seung Kon
2001-01-01
Eu doped YRO 4 (R=As, Nb, P, V)red phosphors were prepared by the combinatorial chemistry method. The quaternary material library of tetrahedron-type composition array was designed to investigate the luminescence of the host material under UV and VUV excitations (254, 147 nm). The photoluminescent characteristics of the samples were comparable to the commercially available red phosphors such as (Y, Gd)BO 3 :Eu 3+ and Y 2 O 3 :Eu 3+ . In view of the luminescence yield, V rich region was found to be optimum under UV excitation. But the results under VUV excitation were different from those of UV excitation, the samples of the composition containing a large amount of P shows the highest luminescence. Especially, higher luminescence was obtained in Y 0.9 (As 0.06 Nb 0.06 P 0.83 V 0.06 )O 4 :Eu 0.1 phosphors than commercial (Y, Gd)BO 3 red phosphors under 147 nm excitation
Dense interstellar cloud chemistry: Basic issues and possible dynamical solution
International Nuclear Information System (INIS)
Prasad, S.S.; Heere, K.R.; Tarafdar, S.P.
1989-01-01
Standing at crossroad of enthusiasm and frustration, dense intertellar cloud chemistry has a squarely posed fundamental problem: Why do the grains appear to play at best a minor role in the chemistry? Grain surface chemistry creates considerable difficulties when the authors treat dense clouds as static objects and ignore the implications of the processes by which the clouds became dense in the first place. A new generation of models which treat chemical and dynamical evolutions concurrently are therefore presented as possible solution to the current frustrations. The proposed modeling philosophy and agenda could make the next decade quite exciting for interstellar chemistry
Maréchal, Eric
2008-09-01
Chemogenomics is the study of the interaction of functional biological systems with exogenous small molecules, or in broader sense the study of the intersection of biological and chemical spaces. Chemogenomics requires expertises in biology, chemistry and computational sciences (bioinformatics, cheminformatics, large scale statistics and machine learning methods) but it is more than the simple apposition of each of these disciplines. Biological entities interacting with small molecules can be isolated proteins or more elaborate systems, from single cells to complete organisms. The biological space is therefore analyzed at various postgenomic levels (genomic, transcriptomic, proteomic or any phenotypic level). The space of small molecules is partially real, corresponding to commercial and academic collections of compounds, and partially virtual, corresponding to the chemical space possibly synthesizable. Synthetic chemistry has developed novel strategies allowing a physical exploration of this universe of possibilities. A major challenge of cheminformatics is to charter the virtual space of small molecules using realistic biological constraints (bioavailability, druggability, structural biological information). Chemogenomics is a descendent of conventional pharmaceutical approaches, since it involves the screening of chemolibraries for their effect on biological targets, and benefits from the advances in the corresponding enabling technologies and the introduction of new biological markers. Screening was originally motivated by the rigorous discovery of new drugs, neglecting and throwing away any molecule that would fail to meet the standards required for a therapeutic treatment. It is now the basis for the discovery of small molecules that might or might not be directly used as drugs, but which have an immense potential for basic research, as probes to explore an increasing number of biological phenomena. Concerns about the environmental impact of chemical industry
Mondal, Milon; Groothuis, Daphne E.; Hirsch, Anna K. H.
2015-01-01
Fragment-based drug design (FBDD) has emerged as an efficient hit-identification and/or-optimization strategy with a higher hit rate than high-throughput screening (HTS). Whereas fragment linking is more challenging, fragment growing has become the preferred fragment-optimization strategy, requiring
Ji, Qing; El-Hamdi, Nadia S.; Miljanic´, Ognjen S?.
2014-01-01
Esters are volatile and pleasantly smelling compounds, commonly used as food additives. Using Ti(OBu)[subscript 4]-catalyzed acyl exchange, we demonstrate a scent transmutation experiment, in which two fragrant esters swap their acyl and alkoxy substituents and are, during the course of a reactive distillation, quantitatively converted into two…
DEFF Research Database (Denmark)
Larsen, Dennis
new types of catalysts were discovered: The 2-aminophenols and the 2-(aminomethyl)benzimidazoles. With aldehyde substrates none of the newly discovered catalysts were as effective as a previously discovered benzenephosphonic acid, but with aromatic ketones, an otherwise challenging class of substrates......, the 2-(aminomethyl)benzimidazoles showed promising efficacies, reaching an hitherto unseen 5-fold rate enhancement for hydrazone formation on model acetophenone at pH 7.4....
Yan, Fang; Liu, Haihong; Liu, Zengrong
2014-01-01
P53 and E2F1 are critical transcription factors involved in the choices between different cell fates including cell differentiation, cell cycle arrest or apoptosis. Recent experiments have shown that two families of microRNAs (miRNAs), p53-responsive miR34 (miRNA-34 a, b and c) and E2F1-inducible miR449 (miRNA-449 a, b and c) are potent inducers of these different fates and might have an important role in sensitizing cancer cells to drug treatment and tumor suppression. Identifying the mechanisms responsible for the combinatorial regulatory roles of these two transcription factors and two miRNAs is an important and challenging problem. Here, based in part on the model proposed in Tongli Zhang et al. (2007), we developed a mathematical model of the decision process and explored the combinatorial regulation between these two transcription factors and two miRNAs in response to DNA damage. By analyzing nonlinear dynamic behaviors of the model, we found that p53 exhibits pulsatile behavior. Moreover, a comparison is given to reveal the subtle differences of the cell fate decision process between regulation and deregulation of miR34 on E2F1. It predicts that miR34 plays a critical role in promoting cell cycle arrest. In addition, a computer simulation result also predicts that the miR449 is necessary for apoptosis in response to sustained DNA damage. In agreement with experimental observations, our model can account for the intricate regulatory relationship between these two transcription factors and two miRNAs in the cell fate decision process after DNA damage. These theoretical results indicate that miR34 and miR449 are effective tumor suppressors and play critical roles in cell fate decisions. The work provides a dynamic mechanism that shows how cell fate decisions are coordinated by two transcription factors and two miRNAs. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology and Clinical Implications. Guest Editor: Yudong Cai
Organoactinide chemistry: synthesis, structure, and solution dynamics
International Nuclear Information System (INIS)
Brennan, J.G.
1985-12-01
This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp 2 MX 2 . Ligand redistribution processes are present throughout the synthetic work, as has often been observed in uranium cyclopentadienyl chemistry. The effects of covalent M-L bonding on the solution and solid state properties of U(III) coordination complexes are considered. In particular, the nature of the more subtle interaction between the metal and the neutral ligand are examined. Using relative basicity data obtained in solution, and solid state structural data (and supplemented by gas phase photoelectron measurements), it is demonstrated that the more electron rich U(III) centers engage in significant U → L π-donation. Trivalent uranium is shown to be capable of acting either as a one- or two-electron reducing agent toward a wide variety of unsaturated organic and inorganic molecules, generating molecular classes unobtainable via traditional synthetic approaches, as well as offering an alternative synthetic approach to molecules accessible via metathesis reactions. Ligand redistribution processes are again observed, but given the information concerning ligand lability, this reactivity pattern is applied to the synthesis of pure materials inaccessible from redox chemistry. 214 refs., 33 figs., 10 tabs
Combinatorial synthesis of natural products
DEFF Research Database (Denmark)
Nielsen, John
2002-01-01
Combinatorial syntheses allow production of compound libraries in an expeditious and organized manner immediately applicable for high-throughput screening. Natural products possess a pedigree to justify quality and appreciation in drug discovery and development. Currently, we are seeing a rapid...... increase in application of natural products in combinatorial chemistry and vice versa. The therapeutic areas of infectious disease and oncology still dominate but many new areas are emerging. Several complex natural products have now been synthesised by solid-phase methods and have created the foundation...... for preparation of combinatorial libraries. In other examples, natural products or intermediates have served as building blocks or scaffolds in the synthesis of complex natural products, bioactive analogues or designed hybrid molecules. Finally, structural motifs from the biologically active parent molecule have...
Kodali, Anuradha
In this thesis, we develop dynamic multiple fault diagnosis (DMFD) algorithms to diagnose faults that are sporadic and coupled. Firstly, we formulate a coupled factorial hidden Markov model-based (CFHMM) framework to diagnose dependent faults occurring over time (dynamic case). Here, we implement a mixed memory Markov coupling model to determine the most likely sequence of (dependent) fault states, the one that best explains the observed test outcomes over time. An iterative Gauss-Seidel coordinate ascent optimization method is proposed for solving the problem. A soft Viterbi algorithm is also implemented within the framework for decoding dependent fault states over time. We demonstrate the algorithm on simulated and real-world systems with coupled faults; the results show that this approach improves the correct isolation rate as compared to the formulation where independent fault states are assumed. Secondly, we formulate a generalization of set-covering, termed dynamic set-covering (DSC), which involves a series of coupled set-covering problems over time. The objective of the DSC problem is to infer the most probable time sequence of a parsimonious set of failure sources that explains the observed test outcomes over time. The DSC problem is NP-hard and intractable due to the fault-test dependency matrix that couples the failed tests and faults via the constraint matrix, and the temporal dependence of failure sources over time. Here, the DSC problem is motivated from the viewpoint of a dynamic multiple fault diagnosis problem, but it has wide applications in operations research, for e.g., facility location problem. Thus, we also formulated the DSC problem in the context of a dynamically evolving facility location problem. Here, a facility can be opened, closed, or can be temporarily unavailable at any time for a given requirement of demand points. These activities are associated with costs or penalties, viz., phase-in or phase-out for the opening or closing of a
Special Issue on Theoretical Chemistry/Chemical Dynamics
Indian Academy of Sciences (India)
2017-07-02
Jul 2, 2017 ... This month's issue of the Journal of Chemical Sciences honours Professor Charusita Chakravarty, who has made immeasurable contributions to theoretical chemistry and chemical dynamics. The editors Biman Bagchi (FASc, FNA, FTWAS; Indian Institute of Science, Bangalore, India), David Clary (FRS; ...
Combinatorial structures to modeling simple games and applications
Molinero, Xavier
2017-09-01
We connect three different topics: combinatorial structures, game theory and chemistry. In particular, we establish the bases to represent some simple games, defined as influence games, and molecules, defined from atoms, by using combinatorial structures. First, we characterize simple games as influence games using influence graphs. It let us to modeling simple games as combinatorial structures (from the viewpoint of structures or graphs). Second, we formally define molecules as combinations of atoms. It let us to modeling molecules as combinatorial structures (from the viewpoint of combinations). It is open to generate such combinatorial structures using some specific techniques as genetic algorithms, (meta-)heuristics algorithms and parallel programming, among others.
Applications of combinatorial optimization
Paschos, Vangelis Th
2013-01-01
Combinatorial optimization is a multidisciplinary scientific area, lying in the interface of three major scientific domains: mathematics, theoretical computer science and management. The three volumes of the Combinatorial Optimization series aims to cover a wide range of topics in this area. These topics also deal with fundamental notions and approaches as with several classical applications of combinatorial optimization. "Applications of Combinatorial Optimization" is presenting a certain number among the most common and well-known applications of Combinatorial Optimization.
Complex Dynamics in Nonequilibrium Economics and Chemistry
Wen, Kehong
Complex dynamics provides a new approach in dealing with economic complexity. We study interactively the empirical and theoretical aspects of business cycles. The way of exploring complexity is similar to that in the study of an oscillatory chemical system (BZ system)--a model for modeling complex behavior. We contribute in simulating qualitatively the complex periodic patterns observed from the controlled BZ experiments to narrow the gap between modeling and experiment. The gap between theory and reality is much wider in economics, which involves studies of human expectations and decisions, the essential difference from natural sciences. Our empirical and theoretical studies make substantial progress in closing this gap. With the help from the new development in nonequilibrium physics, i.e., the complex spectral theory, we advance our technique in detecting characteristic time scales from empirical economic data. We obtain correlation resonances, which give oscillating modes with decays for correlation decomposition, from different time series including S&P 500, M2, crude oil spot prices, and GNP. The time scales found are strikingly compatible with business experiences and other studies in business cycles. They reveal the non-Markovian nature of coherent markets. The resonances enhance the evidence of economic chaos obtained by using other tests. The evolving multi-humped distributions produced by the moving-time -window technique reveal the nonequilibrium nature of economic behavior. They reproduce the American economic history of booms and busts. The studies seem to provide a way out of the debate on chaos versus noise and unify the cyclical and stochastic approaches in explaining business fluctuations. Based on these findings and new expectation formulation, we construct a business cycle model which gives qualitatively compatible patterns to those found empirically. The soft-bouncing oscillator model provides a better alternative than the harmonic oscillator
Dynamic-chemistry-aerosol modelling interaction: the ESCOMPTE 2001 experiment
International Nuclear Information System (INIS)
Cousin, F.
2004-09-01
After most pollution studies independently devoted to gases and aerosols, there now appears an urgent need to consider their interactions. In this view, an aerosol module has been implemented in the Meso-NH-C model to simulate two IOPs documented during the ESCOMPTE campaign which took place in the Marseille/Fos-Berre region in June-July 2001. First, modelled dynamic parameters (winds, temperatures, boundary layer thickness) and gaseous chemistry have been validated with measurements issued from the exhaustive ESCOMPTE database. Sensitivity analysis have also been performed using different gaseous emission inventories at various resolution. These simulations have illustrated the deep impact of both synoptic and local dynamics on observed ozone concentrations on June 24 (IOP2b) in the ESCOMPTE domain. Afterwards, the ORISAM aerosol module has been introduced into the Meso-NH-C model. Dynamics, gaseous chemistry and aerosol processes have thus been coupled on-line. The particulate pollution episode on June 24 (IOP2b) has been characterised through a satisfactory comparison, specially from sub-micron particles, between modelling and measurements at different representative stations in the domain. This study, with validation of the particulate emission inventory has also highlighted the need for future improvements, such as further characterisation of organic and inorganic aerosol species and consideration of coarse particles. Aerosol impact on gaseous chemistry has been preliminary approached in view of future development and modification to be given to the Meso-NH-C model. (author)
Forcing of stratospheric chemistry and dynamics during the Dalton Minimum
Anet, J. G.; Muthers, S.; Rozanov, E.; Raible, C. C.; Peter, T.; Stenke, A.; Shapiro, A. I.; Beer, J.; Steinhilber, F.; Brönnimann, S.; Arfeuille, F.; Brugnara, Y.; Schmutz, W.
2013-11-01
The response of atmospheric chemistry and dynamics to volcanic eruptions and to a decrease in solar activity during the Dalton Minimum is investigated with the fully coupled atmosphere-ocean chemistry general circulation model SOCOL-MPIOM (modeling tools for studies of SOlar Climate Ozone Links-Max Planck Institute Ocean Model) covering the time period 1780 to 1840 AD. We carried out several sensitivity ensemble experiments to separate the effects of (i) reduced solar ultra-violet (UV) irradiance, (ii) reduced solar visible and near infrared irradiance, (iii) enhanced galactic cosmic ray intensity as well as less intensive solar energetic proton events and auroral electron precipitation, and (iv) volcanic aerosols. The introduced changes of UV irradiance and volcanic aerosols significantly influence stratospheric dynamics in the early 19th century, whereas changes in the visible part of the spectrum and energetic particles have smaller effects. A reduction of UV irradiance by 15%, which represents the presently discussed highest estimate of UV irradiance change caused by solar activity changes, causes global ozone decrease below the stratopause reaching as much as 8% in the midlatitudes at 5 hPa and a significant stratospheric cooling of up to 2 °C in the mid-stratosphere and to 6 °C in the lower mesosphere. Changes in energetic particle precipitation lead only to minor changes in the yearly averaged temperature fields in the stratosphere. Volcanic aerosols heat the tropical lower stratosphere, allowing more water vapour to enter the tropical stratosphere, which, via HOx reactions, decreases upper stratospheric and mesospheric ozone by roughly 4%. Conversely, heterogeneous chemistry on aerosols reduces stratospheric NOx, leading to a 12% ozone increase in the tropics, whereas a decrease in ozone of up to 5% is found over Antarctica in boreal winter. The linear superposition of the different contributions is not equivalent to the response obtained in a simulation
Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns
International Nuclear Information System (INIS)
Wishart, J.F.
2011-01-01
Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs generally have low volatilities and are combustion-resistant, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of primary radiation chemistry, charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of reactions and product distributions. We study these issues by characterization of primary radiolysis products and measurements of their yields and reactivity, quantification of electron solvation dynamics and scavenging of electrons in different states of solvation. From this knowledge we wish to learn how to predict radiolytic mechanisms and control them or mitigate their effects on the properties of materials used in nuclear fuel processing, for example, and to apply IL radiation chemistry to answer questions about general chemical reactivity in ionic liquids that will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that the slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increase the importance of pre-solvated electron reactivity and consequently alter product distributions and subsequent chemistry. This difference from conventional solvents has profound effects on predicting and controlling radiolytic yields
Concepts of combinatorial optimization
Paschos, Vangelis Th
2014-01-01
Combinatorial optimization is a multidisciplinary scientific area, lying in the interface of three major scientific domains: mathematics, theoretical computer science and management. The three volumes of the Combinatorial Optimization series aim to cover a wide range of topics in this area. These topics also deal with fundamental notions and approaches as with several classical applications of combinatorial optimization.Concepts of Combinatorial Optimization, is divided into three parts:- On the complexity of combinatorial optimization problems, presenting basics about worst-case and randomi
Hu, T C
2002-01-01
Newly enlarged, updated second edition of a valuable text presents algorithms for shortest paths, maximum flows, dynamic programming and backtracking. Also discusses binary trees, heuristic and near optimums, matrix multiplication, and NP-complete problems. 153 black-and-white illus. 23 tables.Newly enlarged, updated second edition of a valuable, widely used text presents algorithms for shortest paths, maximum flows, dynamic programming and backtracking. Also discussed are binary trees, heuristic and near optimums, matrix multiplication, and NP-complete problems. New to this edition: Chapter 9
Dynamic light scattering with applications to chemistry, biology, and physics
Berne, Bruce J
2000-01-01
Lasers play an increasingly important role in a variety of detection techniques, making inelastic light scattering a tool of growing value in the investigation of dynamic and structural problems in chemistry, biology, and physics. Until the initial publication of this work, however, no monograph treated the principles behind current developments in the field.This volume presents a comprehensive introduction to the principles underlying laser light scattering, focusing on the time dependence of fluctuations in fluid systems; it also serves as an introduction to the theory of time correlation f
National Research Council Canada - National Science Library
Nusca, Michael J; Chen, Chiung-Chu; McQuaid, Michael J
2007-01-01
.... Computational fluid dynamics is employed to model the chemically reacting flow within a system's combustion chamber, and computational chemistry is employed to characterize propellant physical and reactive properties...
Molecular Dynamics Studies of Thermal Induced Chemistry in Tatb
Quenneville, J.; Germann, T. C.; Thompson, A. P.; Kober, E. M.
2007-12-01
A reactive force field (ReaxFF) is used with molecular dynamics to probe the chemistry induced by intense heating (`accelerated cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 32-molecule simulations, we calculate the reaction rate as a function of temperature and compare the Arrhenius-predicted activation energy with experiment. Decomposition product evolution (mainly N2, H2O, CO2 and graphitic carbon clusters) is followed using a 576-molecule larger simulation, which also illustrates the effect of system size on both carbon clustering and reaction rate.
Influence of chemistry on wetting dynamics of nanotextured hydrophobic surfaces.
Di Mundo, Rosa; Palumbo, Fabio; d'Agostino, Riccardo
2010-04-06
In this work, the role of a chemical parameter, such as the degree of fluorination, on the wetting behavior of nanotextured hydrophobic surfaces is investigated. Texture and chemistry tuning of the surfaces has been accomplished with single batch radiofrequency low-pressure plasma processes. Polystyrene substrates have been textured by CF(4) plasma etching and subsequently covered by thin films with a tunable F-to-C ratio, obtained in discharges fed with C(4)F(8)-C(2)H(4). Measurements of wetting dynamics reveal a regime transition from adhesive-hydrophobic to slippery-superhydrophobic, i.e., from wet to non wet states, as the F-to-C rises at constant topography. Such achievements are strengthened by calculation of the solid fraction of surface water contact area applying Cassie-Baxter advancing and receding equations to water contact angle data of textured and flat reference surfaces.
Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns
International Nuclear Information System (INIS)
Wishart, J.F.
2008-01-01
Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate
IONIC LIQUIDS: RADIATION CHEMISTRY, SOLVATION DYNAMICS AND REACTIVITY PATTERNS
International Nuclear Information System (INIS)
WISHART, J.F.
2007-01-01
energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are generally nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of applications listed above. Very early in our radiolysis studies it became evident that slow solvation dynamics of the excess electron in ILs (which vary over a wide viscosity range) increases the importance of pre-solvated electron reactivity and consequently alters product distributions. Parallel studies of IL solvation phenomena using coumarin-153 dynamic Stokes shifts and polarization anisotropy decay rates are done to compare with electron solvation studies and to evaluate the influence of ILs on charge transport processes. Methods. Picosecond pulse radiolysis studies at BNL
Combinatorial commutative algebra
Miller, Ezra
2005-01-01
Offers an introduction to combinatorial commutative algebra, focusing on combinatorial techniques for multigraded polynomial rings, semigroup algebras, and determined rings. The chapters in this work cover topics ranging from homological invariants of monomial ideals and their polyhedral resolutions, to tools for studying algebraic varieties.
Combinatorial enzyme technology for the conversion of agricultural fibers to functional properties
The concept of combinatorial chemistry has received little attention in agriculture and food research, although its applications in this area were described more than fifteen years ago (1, 2). More recently, interest in the use of combinatorial chemistry in agrochemical discovery has been revitalize...
Chin, Gordon
2011-01-01
Vesper conducts a focused investigation of the chemistry and dynamics of the middle atmosphere of our sister planet- from the base of the global cloud cover to the lower thermosphere. The middle atmosphere controls the stability of the Venus climate system. Vesper determines what processes maintain the atmospheric chemical stability, cause observed variability of chemical composition, control the escape of water, and drive the extreme super-rotation. The Vesper science investigation provides a unique perspective on the Earth environment due to the similarities in the middle atmosphere processes of both Venus and the Earth. Understanding key distinctions and similarities between Venus and Earth will increase our knowledge of how terrestrial planets evolve along different paths from nearly identical initial conditions.
Neural Meta-Memes Framework for Combinatorial Optimization
Song, Li Qin; Lim, Meng Hiot; Ong, Yew Soon
In this paper, we present a Neural Meta-Memes Framework (NMMF) for combinatorial optimization. NMMF is a framework which models basic optimization algorithms as memes and manages them dynamically when solving combinatorial problems. NMMF encompasses neural networks which serve as the overall planner/coordinator to balance the workload between memes. We show the efficacy of the proposed NMMF through empirical study on a class of combinatorial problem, the quadratic assignment problem (QAP).
Design of a Dynamic Undergraduate Green Chemistry Course
Kennedy, Sarah A.
2016-01-01
The green chemistry course taught at Westminster College (PA) incorporates nontraditional teaching techniques and texts to educate future chemists about the importance of using green chemistry principles. The course is designed to introduce green chemistry concepts and demonstrate their inherent necessity by discussing historical missteps by the…
Flame Dynamics and Chemistry in LRE Combustion Instability
2016-12-22
negative temperature coefficient phenomenon and engine knock. In this work, the coupling of cool flame chemistry and convective– diffusive transport...note, practical engine conditions are highly turbulent, and the autoignition phenomenon depends on both chemistry and turbulent mixing. For example...negative temperature coefficient (NTC) phenomenon and engine knock. In this work, the coupling of cool flame chemistry and convective–diffusive
Energy Technology Data Exchange (ETDEWEB)
Zhao, Yingdi; Tan, Ke; Zhou, Yan; Ye, Zhaoyang, E-mail: zhaoyangye@ecust.edu.cn; Tan, Wen-Song
2016-02-01
Biomaterial properties play significant roles in controlling cellular behaviors. The objective of the present study was to investigate how pore size and surface chemistry of three-dimensional (3D) porous scaffolds regulate the fate of mesenchymal stem cells (MSCs) in vitro in combination. First, on poly(ε-caprolactone) (PCL) films, the hydrolytic treatment was found to stimulate the adhesion, spreading and proliferation of human MSCs (hMSCs) in comparison with pristine films, while the aminolysis showed mixed effects. Then, 3D porous PCL scaffolds with varying pore sizes (100–200 μm, 200–300 μm and 300–450 μm) were fabricated and subjected to either hydrolysis or aminolysis. It was found that a pore size of 200–300 μm with hydrolysis in 3D scaffolds was the most favorable condition for growth of hMSCs. Importantly, while a pore size of 200–300 μm with hydrolysis for 1 h supported the best osteogenic differentiation of hMSCs, the chondrogenic differentiation was greatest in scaffolds with a pore size of 300–450 μm and treated with aminolysis for 1 h. Taken together, these results suggest that surface chemistry and pore size of 3D porous scaffolds may potentially have a synergistic impact on the behaviors of MSCs. - Highlights: • Surface chemistry of poly(ε-caprolactone) films actively modulates MSC behaviors. • Varying surface chemistry and pore size in combination is enabled in 3D scaffolds. • Surface chemistry and pore size potentially dictate MSC fates in synergy.
International Nuclear Information System (INIS)
Zhao, Yingdi; Tan, Ke; Zhou, Yan; Ye, Zhaoyang; Tan, Wen-Song
2016-01-01
Biomaterial properties play significant roles in controlling cellular behaviors. The objective of the present study was to investigate how pore size and surface chemistry of three-dimensional (3D) porous scaffolds regulate the fate of mesenchymal stem cells (MSCs) in vitro in combination. First, on poly(ε-caprolactone) (PCL) films, the hydrolytic treatment was found to stimulate the adhesion, spreading and proliferation of human MSCs (hMSCs) in comparison with pristine films, while the aminolysis showed mixed effects. Then, 3D porous PCL scaffolds with varying pore sizes (100–200 μm, 200–300 μm and 300–450 μm) were fabricated and subjected to either hydrolysis or aminolysis. It was found that a pore size of 200–300 μm with hydrolysis in 3D scaffolds was the most favorable condition for growth of hMSCs. Importantly, while a pore size of 200–300 μm with hydrolysis for 1 h supported the best osteogenic differentiation of hMSCs, the chondrogenic differentiation was greatest in scaffolds with a pore size of 300–450 μm and treated with aminolysis for 1 h. Taken together, these results suggest that surface chemistry and pore size of 3D porous scaffolds may potentially have a synergistic impact on the behaviors of MSCs. - Highlights: • Surface chemistry of poly(ε-caprolactone) films actively modulates MSC behaviors. • Varying surface chemistry and pore size in combination is enabled in 3D scaffolds. • Surface chemistry and pore size potentially dictate MSC fates in synergy.
Teixidó, Meritxell; Belda, Ignasi; Zurita, Esther; Llorà, Xavier; Fabre, Myriam; Vilaró, Senén; Albericio, Fernando; Giralt, Ernest
2005-12-01
The use of high-throughput methods in drug discovery allows the generation and testing of a large number of compounds, but at the price of providing redundant information. Evolutionary combinatorial chemistry combines the selection and synthesis of biologically active compounds with artificial intelligence optimization methods, such as genetic algorithms (GA). Drug candidates for the treatment of central nervous system (CNS) disorders must overcome the blood-brain barrier (BBB). This paper reports a new genetic algorithm that searches for the optimal physicochemical properties for peptide transport across the blood-brain barrier. A first generation of peptides has been generated and synthesized. Due to the high content of N-methyl amino acids present in most of these peptides, their syntheses were especially challenging due to over-incorporations, deletions and DKP formations. Distinct fragmentation patterns during peptide cleavage have been identified. The first generation of peptides has been studied by evaluation techniques such as immobilized artificial membrane chromatography (IAMC), a cell-based assay, log Poctanol/water calculations, etc. Finally, a second generation has been proposed. (c) 2005 European Peptide Society and John Wiley & Sons, Ltd.
Integer and combinatorial optimization
Nemhauser, George L
1999-01-01
Rave reviews for INTEGER AND COMBINATORIAL OPTIMIZATION ""This book provides an excellent introduction and survey of traditional fields of combinatorial optimization . . . It is indeed one of the best and most complete texts on combinatorial optimization . . . available. [And] with more than 700 entries, [it] has quite an exhaustive reference list.""-Optima ""A unifying approach to optimization problems is to formulate them like linear programming problems, while restricting some or all of the variables to the integers. This book is an encyclopedic resource for such f
Theoretical study of reaction dynamics in radiation chemistry
International Nuclear Information System (INIS)
Tachiya, Masanori
2008-01-01
The period from late 1950's to early 1970's was golden age of radiation chemistry. During this period the hydrated electron was discovered, various new phenomena were found in ionic processes in liquid hydrocarbons, and the trapped electron and electron tunneling were discovered in organic glasses. In those days radiation chemistry was a vast treasure-house of theoretical problems. We could find not only problems special to radiation chemistry but also many problems interesting as general physical chemistry. In this review I explain how some theoretical problems discovered in the field of radiation chemistry have evolved into those of general physical chemistry, with special emphasis on my own work. (author)
Ionic liquids: radiation chemistry, solvation dynamics and reactivity patterns
International Nuclear Information System (INIS)
Wishart, J.F.; Funston, A.M.; Szreder, T.
2006-01-01
Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of energy production, chemical industry and environmental applications. Pulse radiolysis of [R 4 N][NTf 2 ] [R 4 N][N(CN) 2 ], and [R 4 P][N(CN) 2 ] ionic liquids produces solvated electrons that absorb over a broad range in the near infrared and persisting for hundreds of nanoseconds. Systematic cation variation shows that solvated electron's spectroscopic properties depend strongly on the lattice structure of the ionic liquid. Very early in our radiolysis studies it became evident that
Combinatorial Solid-Phase Synthesis of Balanol Analogues
DEFF Research Database (Denmark)
Nielsen, John; Lyngsø, Lars Ole
1996-01-01
The natural product balanol has served as a template for the design and synthesis of a combinatorial library using solid-phase chemistry. Using a retrosynthetic analysis, the structural analogues have been assembled from three relatively accessible building blocks. The solid-phase chemistry inclu...
Nonparametric combinatorial sequence models.
Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa
2011-11-01
This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.
Dynamic Covalent Chemistry of Carbon Dioxide: Opportunities to Address Environmental Issues.
Septavaux, Jean; Germain, Geoffroy; Leclaire, Julien
2017-07-18
equilibrium. This equilibrium may involve covalent or noncovalent bond formation between a supplementary species and either the unloaded reactant or the CO 2 -loaded product. Thereby, this new reactive species may act as a CO 2 capture agonist or antagonist by either thermodynamically favoring the carbamation or decarbamation direction. Indeed, superagonism, the increase of CO 2 loading per amine site upon carbamation beyond the theoretical limit of 0.5, can be achieved using tightly bound cationic metal counterions. In all cases, upon binding and adduct formation, a mutual selection process occurs between one member of the CO 2 -based dynamic combinatorial library and one agonist or antagonist, which can itself be contained in a complex mixture of analogues. If this adduct is the only species that, upon formation, can self-aggregate into a separate solid phase, selection and binding are accompanied by translocation, rendering the purification procedure operationally straightforward. This general strategy, based on a simple design of coupled molecular systems, may easily be implemented within new, disruptive technologies for selective extraction of target molecules, thereby providing a substantial environmental and economic benefit.
Combinatorial stresses kill pathogenic Candida species
Kaloriti, Despoina; Tillmann, Anna; Cook, Emily; Jacobsen, Mette; You, Tao; Lenardon, Megan; Ames, Lauren; Barahona, Mauricio; Chandrasekaran, Komelapriya; Coghill, George; Goodman, Daniel; Gow, Neil A. R.; Grebogi, Celso; Ho, Hsueh-Lui; Ingram, Piers; McDonagh, Andrew; De Moura, Alessandro P. S.; Pang, Wei; Puttnam, Melanie; Radmaneshfar, Elahe; Romano, Maria Carmen; Silk, Daniel; Stark, Jaroslav; Stumpf, Michael; Thiel, Marco; Thorne, Thomas; Usher, Jane; Yin, Zhikang; Haynes, Ken; Brown, Alistair J. P.
2012-01-01
Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses. In the wild, cells are frequently exposed simultaneously to combinations of these stresses and yet the effects of such combinatorial stresses have not been explored. We have developed a common experimental platform to facilitate the comparison of combinatorial stress responses in C. glabrata and C. albicans. This platform is based on the growth of cells in buffered rich medium at 30°C, and was used to define relatively low, medium and high doses of osmotic (NaCl), oxidative (H 2O2) and nitrosative stresses (e.g., dipropylenetriamine (DPTA)-NONOate). The effects of combinatorial stresses were compared with the corresponding individual stresses under these growth conditions. We show for the first time that certain combinations of combinatorial stress are especially potent in terms of their ability to kill C. albicans and C. glabrata and/or inhibit their growth. This was the case for combinations of osmotic plus oxidative stress and for oxidative plus nitrosative stress. We predict that combinatorial stresses may be highly signif cant in host defences against these pathogenic yeasts. PMID:22463109
Introduction to combinatorial designs
Wallis, WD
2007-01-01
Combinatorial theory is one of the fastest growing areas of modern mathematics. Focusing on a major part of this subject, Introduction to Combinatorial Designs, Second Edition provides a solid foundation in the classical areas of design theory as well as in more contemporary designs based on applications in a variety of fields. After an overview of basic concepts, the text introduces balanced designs and finite geometries. The author then delves into balanced incomplete block designs, covering difference methods, residual and derived designs, and resolvability. Following a chapter on the e
International Nuclear Information System (INIS)
Ferris, L.M.
1975-01-01
The chemical research and development efforts related to the design and ultimate operation of molten-salt breeder reactor systems are concentrated on fuel- and coolant-salt chemistry, including the development of analytical methods for use in these systems. The chemistry of tellurium in fuel salt is being studied to help elucidate the role of this element in the intergranular cracking of Hastelloy N. Studies were continued of the effect of oxygen-containing species on the equilibrium between dissolved UF 3 and dissolved UF 4 , and, in some cases, between the dissolved uranium fluorides and graphite, and the UC 2 . Several aspects of coolant-salt chemistry are under investigation. Hydroxy and oxy compounds that could be formed in molten NaBF 4 are being synthesized and characterized. Studies of the chemistry of chromium (III) compounds in fluoroborate melts were continued as part of a systematic investigation of the corrosion of structural alloys by coolant salt. An in-line voltammetric method for determining U 4+ /U 3+ ratios in fuel salt was tested in a forced-convection loop over a six-month period. (LK)
Physical Chemistry of Reaction Dynamics in Ionic Liquid
Energy Technology Data Exchange (ETDEWEB)
Maroncelli, Mark [Pennsylvania State Univ., University Park, PA (United States)
2016-10-02
Work completed over the past year mainly involves finishing studies related to solvation dynamics in ionic liquids, amplifying and extending our initial PFG-NMR work on solute diffusion, and learning how to probe rotational dynamics in ionic liquids.
Infinitary Combinatory Reduction Systems
DEFF Research Database (Denmark)
Ketema, Jeroen; Simonsen, Jakob Grue
2011-01-01
We define infinitary Combinatory Reduction Systems (iCRSs), thus providing the first notion of infinitary higher-order rewriting. The systems defined are sufficiently general that ordinary infinitary term rewriting and infinitary ¿-calculus are special cases. Furthermore,we generalise a number...
Manipulating Combinatorial Structures.
Labelle, Gilbert
This set of transparencies shows how the manipulation of combinatorial structures in the context of modern combinatorics can easily lead to interesting teaching and learning activities at every level of education from elementary school to university. The transparencies describe: (1) the importance and relations of combinatorics to science and…
Introduction to combinatorial geometry
International Nuclear Information System (INIS)
Gabriel, T.A.; Emmett, M.B.
1985-01-01
The combinatorial geometry package as used in many three-dimensional multimedia Monte Carlo radiation transport codes, such as HETC, MORSE, and EGS, is becoming the preferred way to describe simple and complicated systems. Just about any system can be modeled using the package with relatively few input statements. This can be contrasted against the older style geometry packages in which the required input statements could be large even for relatively simple systems. However, with advancements come some difficulties. The users of combinatorial geometry must be able to visualize more, and, in some instances, all of the system at a time. Errors can be introduced into the modeling which, though slight, and at times hard to detect, can have devastating effects on the calculated results. As with all modeling packages, the best way to learn the combinatorial geometry is to use it, first on a simple system then on more complicated systems. The basic technique for the description of the geometry consists of defining the location and shape of the various zones in terms of the intersections and unions of geometric bodies. The geometric bodies which are generally included in most combinatorial geometry packages are: (1) box, (2) right parallelepiped, (3) sphere, (4) right circular cylinder, (5) right elliptic cylinder, (6) ellipsoid, (7) truncated right cone, (8) right angle wedge, and (9) arbitrary polyhedron. The data necessary to describe each of these bodies are given. As can be easily noted, there are some subsets included for simplicity
Beyond Problem-Based Learning: Using Dynamic PBL in Chemistry
Overton, Tina L.; Randles, Christopher A.
2015-01-01
This paper describes the development and implementation of a novel pedagogy, dynamic problem-based learning. The pedagogy utilises real-world problems that evolve throughout the problem-based learning activity and provide students with choice and different data sets. This new dynamic problem-based learning approach was utilised to teach…
International Nuclear Information System (INIS)
Ferris, L.M.
1976-01-01
Research progress is reported in programs on fuel-salt chemistry, properties of compounds in the Li--Te system, Te spectroscopy UF 4 --H equilibria, porous electrode studies of molten salts, fuel salt-coolant salt reactions, thermodynamic properties of transition-metal fluorides, and properties of sodium fluoroborate. Developmental work on analytical methods is summarized including in-line analysis of molten MSBR fuel, analysis of coolant-salts for tritium, analysis of molten LiF--BeF 2 --ThF 4 for Fe and analysis of LiF--BeF--ThF 4 for Te
Chemistry in interstellar space. [environment characteristics influencing reaction dynamics
Donn, B.
1973-01-01
The particular characteristics of chemistry in interstellar space are determined by the unique environmental conditions involved. Interstellar matter is present at extremely low densities. Large deviations from thermodynamic equilibrium are, therefore, to be expected. A relatively intense ultraviolet radiation is present in many regions. The temperatures are in the range from 5 to 200 K. Data concerning the inhibiting effect of small activation energies in interstellar clouds are presented in a table. A summary of measured activation energies or barrier heights for exothermic exchange reactions is also provided. Problems of molecule formation are discussed, taking into account gas phase reactions and surface catalyzed processes.
Combinatorial Chemistry of Piperidine Based Carbohydrate Mimics
DEFF Research Database (Denmark)
Byrgesen, Elisabeth Vang; Nielsen, John; Willart, Marianne
1997-01-01
Piperidine carboxylic acids and 4-hydroxypiperidine-3-carboxylic acid, the latter obtained from bakers yeast reduction of the corresponding piperidone, were coupled in solid-phase synthesis to form simplified oligosaccharide analogues. A split-and-mix synthesis approach was used to create small c...
Gas dynamics, optics and chemistry of an aircraft condensable wake
Energy Technology Data Exchange (ETDEWEB)
Grinats, E.S.; Kashevarov, A.V.; Stasenko, A.L. [Central Aerohydrodynamic Inst., Zhukovsky (Russian Federation)
1997-12-31
Prediction of the properties of a jet-and-vortex wake from an individual airplane is of great interest as the first step to assessment of the possible global changes in the atmosphere due to the world civil aviation. Several mathematical models of the different regions of an aircraft wake and corresponding numerical results are presented. The axisymmetric exhaust jet was simulated on the base of the well-known k-{epsilon} model of turbulence. Jet chemistry was investigated on the base of kinetic scheme of the gas phase reactions of enriched by including chemisorption by water droplets of several species and by taking into account of the photochemical processes. In the 3D far wake model, the numerical results for distribution of species exhausted by the engines and entrapped by the velocity field of two parallel vortices are shown. (R.P.) 7 refs.
Gas dynamics, optics and chemistry of an aircraft condensable wake
Energy Technology Data Exchange (ETDEWEB)
Grinats, E S; Kashevarov, A V; Stasenko, A L [Central Aerohydrodynamic Inst., Zhukovsky (Russian Federation)
1998-12-31
Prediction of the properties of a jet-and-vortex wake from an individual airplane is of great interest as the first step to assessment of the possible global changes in the atmosphere due to the world civil aviation. Several mathematical models of the different regions of an aircraft wake and corresponding numerical results are presented. The axisymmetric exhaust jet was simulated on the base of the well-known k-{epsilon} model of turbulence. Jet chemistry was investigated on the base of kinetic scheme of the gas phase reactions of enriched by including chemisorption by water droplets of several species and by taking into account of the photochemical processes. In the 3D far wake model, the numerical results for distribution of species exhausted by the engines and entrapped by the velocity field of two parallel vortices are shown. (R.P.) 7 refs.
Aqueous vanadium ion dynamics relevant to bioinorganic chemistry: A review.
Kustin, Kenneth
2015-06-01
Aqueous solutions of the four highest vanadium oxidation states exhibit four diverse colors, which only hint at the diverse reactions that these ions can undergo. Cationic vanadium ions form complexes with ligands; anionic vanadium ions form complexes with ligands and self-react to form isopolyanions. All vanadium species undergo oxidation-reduction reactions. With a few exceptions, elucidation of the dynamics of these reactions awaited the development of fast reaction techniques before the kinetics of elementary ligation, condensation, reduction, and oxidation of the aqueous vanadium ions could be investigated. As the biological roles played by endogenous and therapeutic vanadium expand, it is appropriate to bring the results of the diverse kinetics studies under one umbrella. To achieve this goal this review presents a systematic examination of elementary aqueous vanadium ion dynamics. Copyright © 2014 Elsevier Inc. All rights reserved.
Urbanization Changes the Temporal Dynamics of Nutrients and Water Chemistry
Steele, M.; Badgley, B.
2017-12-01
Recent studies find that urban development alters the seasonal dynamics of nutrient concentrations, where the highest concentrations of nitrogen occurred during the winter in urban watersheds, rather than the summer. However, the effects of urbanization on the seasonal concentrations of other nutrients and chemical components is unknown. Therefore, to determine how urbanization changes the seasonal dynamics, once a week we measured concentrations of dissolved organic carbon (DOC), nutrients (NO3, DON, TN, PO4), base cations (Ca, Mg, Na, K), anions (F, Cl, SO4), pH, sediment, temperature, conductivity, and dissolved oxygen (DO) of nine urban, agricultural, and minimally developed watersheds in southwest Virginia, USA. We found that urbanization disrupted the seasonal dynamics of all metrics, except DON, PO4, Ca, sediment, and DO, where some shifted to high concentrations during the winter (Cl, conductivity), highs during late winter or spring (DOC, Na), a season low (TN, SO4, NO3) or high (NH4) during the summer, or remained more constant throughout the year compared to the reference watersheds (Mg, K, pH). The complex changes in seasonal dynamics coincide with a decoupling of common correlations between constituents; for example, DO and NO3 are negatively correlated in reference watersheds (NO3 increases, DO decreases), but positively correlated in urban watersheds. These results suggest that as watersheds become more intensely developed, the influence of natural drivers like temperature and vegetation become steadily overcome by the influence of urban drivers like deicing salts and wastewater leakage, which exert increasing control of seasonal water quality and aquatic habitat.
Dynamics and Chemistry in Jovian Atmospheres: 2D Hydrodynamical Simulations
Bordwell, B. R.; Brown, B. P.; Oishi, J.
2016-12-01
A key component of our understanding of the formation and evolution of planetary systems is chemical composition. Problematically, however, in the atmospheres of cooler gas giants, dynamics on the same timescale as chemical reactions pull molecular abundances out of thermochemical equilibrium. These disequilibrium abundances are treated using what is known as the "quench" approximation, based upon the mixing length theory of convection. The validity of this approximation is questionable, though, as the atmospheres of gas giants encompass two distinct dynamic regimes: convective and radiative. To resolve this issue, we conduct 2D hydrodynamical simulations using the state-of-the-art pseudospectral simulation framework Dedalus. In these simulations, we solve the fully compressible equations of fluid motion in a local slab geometry that mimics the structure of a planetary atmosphere (convective zone underlying a radiative zone). Through the inclusion of passive tracers, we explore the transport properties of both regimes, and assess the validity of the classical eddy diffusion parameterization. With the addition of active tracers, we examine the interactions between dynamical and chemical processes, and generate prescriptions for the observational community. By providing insight into mixing and feedback mechanisms in Jovian atmospheres, this research lays a solid foundation for future global simulations and the construction of physically-sound models for current and future observations.
International Nuclear Information System (INIS)
Ferris, L.M.
1975-01-01
Research and development activities dealing with the chemical problems related to design and ultimate operation of molten-salt reactor systems are described. An experimental test stand was constructed to expose metallurgical test specimens to Te 2 vapor at defined temperatures and deposition rates. To better define the chemistry of fluoroborate coolant, several aspects are being investigated. The behavior of hydroxy and oxy compounds in molten NaBF 4 is being investigated to define reactions and compounds that may be involved in corrosion and/or could be involved in methods for trapping tritium. Two corrosion products of Hastelloy N, Na 3 CrF 6 and Na 5 Cr 3 F 14 , were identified from fluoroborate systems. The evaluation of fluoroborate and alternate coolants continued. Research on the behavior of hydrogen and its isotopes is summarized. The solubilities of hydrogen, deuterium, and helium in Li 2 BeF 4 are very low. The sorption of tritium on graphite was found to be significant (a few milligrams of tritium per kilogram of graphite), possibly providing a means of sequestering a portion of the tritium produced. Development of analytical methods continued with emphasis on voltammetric and spectrophotometric techniques for the in-line analysis of corrosion products such as Fe 2+ and Cr 3+ and the determination of the U 3+ /U 4+ ratio in MSBR fuel salt. Similar studies were conducted with the NaBF 4 --NaF coolant salt. Information developed during the previous operation of the CSTF has been assessed and used to formulate plans for evaluation of in-line analytical methods in future CSTF operations. Electroanalytical and spectrophotometric research suggests that an electroactive protonic species is present in molten NaBF 4 --NaF, and that this species rapidly equilibrates with a volatile proton-containing species. Data obtained from the CSTF indicated that tritium was concentrated in the volatile species. (JGB)
Directory of Open Access Journals (Sweden)
Igor V. Protasov
2013-09-01
$\\Delta(A=\\{g\\in G:|gA\\cap A|=\\infty\\}$. The mapping $\\Delta:\\mathcal{P}_G\\rightarrow\\mathcal{P}_G$, $A\\mapsto\\Delta(A$, is called a combinatorial derivation and can be considered as an analogue of the topological derivation $d:\\mathcal{P}_X\\rightarrow\\mathcal{P}_X$, $A\\mapsto A^d$, where $X$ is a topological space and $A^d$ is the set of all limit points of $A$. Content: elementary properties, thin and almost thin subsets, partitions, inverse construction and $\\Delta$-trajectories, $\\Delta$ and $d$.
Boltzmann Oracle for Combinatorial Systems
Pivoteau , Carine; Salvy , Bruno; Soria , Michèle
2008-01-01
International audience; Boltzmann random generation applies to well-deﬁned systems of recursive combinatorial equations. It relies on oracles giving values of the enumeration generating series inside their disk of convergence. We show that the combinatorial systems translate into numerical iteration schemes that provide such oracles. In particular, we give a fast oracle based on Newton iteration.
Mitjana, Margarida
2018-01-01
This book contains the notes of the lectures delivered at an Advanced Course on Combinatorial Matrix Theory held at Centre de Recerca Matemàtica (CRM) in Barcelona. These notes correspond to five series of lectures. The first series is dedicated to the study of several matrix classes defined combinatorially, and was delivered by Richard A. Brualdi. The second one, given by Pauline van den Driessche, is concerned with the study of spectral properties of matrices with a given sign pattern. Dragan Stevanović delivered the third one, devoted to describing the spectral radius of a graph as a tool to provide bounds of parameters related with properties of a graph. The fourth lecture was delivered by Stephen Kirkland and is dedicated to the applications of the Group Inverse of the Laplacian matrix. The last one, given by Ángeles Carmona, focuses on boundary value problems on finite networks with special in-depth on the M-matrix inverse problem.
Cryptographic Combinatorial Securities Exchanges
Thorpe, Christopher; Parkes, David C.
We present a useful new mechanism that facilitates the atomic exchange of many large baskets of securities in a combinatorial exchange. Cryptography prevents information about the securities in the baskets from being exploited, enhancing trust. Our exchange offers institutions who wish to trade large positions a new alternative to existing methods of block trading: they can reduce transaction costs by taking advantage of other institutions’ available liquidity, while third party liquidity providers guarantee execution—preserving their desired portfolio composition at all times. In our exchange, institutions submit encrypted orders which are crossed, leaving a “remainder”. The exchange proves facts about the portfolio risk of this remainder to third party liquidity providers without revealing the securities in the remainder, the knowledge of which could also be exploited. The third parties learn either (depending on the setting) the portfolio risk parameters of the remainder itself, or how their own portfolio risk would change if they were to incorporate the remainder into a portfolio they submit. In one setting, these third parties submit bids on the commission, and the winner supplies necessary liquidity for the entire exchange to clear. This guaranteed clearing, coupled with external price discovery from the primary markets for the securities, sidesteps difficult combinatorial optimization problems. This latter method of proving how taking on the remainder would change risk parameters of one’s own portfolio, without revealing the remainder’s contents or its own risk parameters, is a useful protocol of independent interest.
Balancing focused combinatorial libraries based on multiple GPCR ligands
Soltanshahi, Farhad; Mansley, Tamsin E.; Choi, Sun; Clark, Robert D.
2006-08-01
G-Protein coupled receptors (GPCRs) are important targets for drug discovery, and combinatorial chemistry is an important tool for pharmaceutical development. The absence of detailed structural information, however, limits the kinds of combinatorial design techniques that can be applied to GPCR targets. This is particularly problematic given the current emphasis on focused combinatorial libraries. By linking an incremental construction method (OptDesign) to the very fast shape-matching capability of ChemSpace, we have created an efficient method for designing targeted sublibraries that are topomerically similar to known actives. Multi-objective scoring allows consideration of multiple queries (actives) simultaneously. This can lead to a distribution of products skewed towards one particular query structure, however, particularly when the ligands of interest are quite dissimilar to one another. A novel pivoting technique is described which makes it possible to generate promising designs even under those circumstances. The approach is illustrated by application to some serotonergic agonists and chemokine antagonists.
Coupling dynamics and chemistry in the air pollution modelling of street canyons: A review.
Zhong, Jian; Cai, Xiao-Ming; Bloss, William James
2016-07-01
Air pollutants emitted from vehicles in street canyons may be reactive, undergoing mixing and chemical processing before escaping into the overlying atmosphere. The deterioration of air quality in street canyons occurs due to combined effects of proximate emission sources, dynamical processes (reduced dispersion) and chemical processes (evolution of reactive primary and formation of secondary pollutants). The coupling between dynamics and chemistry plays a major role in determining street canyon air quality, and numerical model approaches to represent this coupling are reviewed in this article. Dynamical processes can be represented by Computational Fluid Dynamics (CFD) techniques. The choice of CFD approach (mainly the Reynolds-Averaged Navier-Stokes (RANS) and Large-Eddy Simulation (LES) models) depends on the computational cost, the accuracy required and hence the application. Simplified parameterisations of the overall integrated effect of dynamics in street canyons provide capability to handle relatively complex chemistry in practical applications. Chemical processes are represented by a chemical mechanism, which describes mathematically the chemical removal and formation of primary and secondary species. Coupling between these aspects needs to accommodate transport, dispersion and chemical reactions for reactive pollutants, especially fast chemical reactions with time scales comparable to or shorter than those of typical turbulent eddies inside the street canyon. Different approaches to dynamical and chemical coupling have varying strengths, costs and levels of accuracy, which must be considered in their use for provision of reference information concerning urban canopy air pollution to stakeholders considering traffic and urban planning policies. Copyright © 2016 Elsevier Ltd. All rights reserved.
Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
Combinatorial optimization games
Energy Technology Data Exchange (ETDEWEB)
Deng, X. [York Univ., North York, Ontario (Canada); Ibaraki, Toshihide; Nagamochi, Hiroshi [Kyoto Univ. (Japan)
1997-06-01
We introduce a general integer programming formulation for a class of combinatorial optimization games, which immediately allows us to improve the algorithmic result for finding amputations in the core (an important solution concept in cooperative game theory) of the network flow game on simple networks by Kalai and Zemel. An interesting result is a general theorem that the core for this class of games is nonempty if and only if a related linear program has an integer optimal solution. We study the properties for this mathematical condition to hold for several interesting problems, and apply them to resolve algorithmic and complexity issues for their cores along the line as put forward in: decide whether the core is empty; if the core is empty, find an imputation in the core; given an imputation x, test whether x is in the core. We also explore the properties of totally balanced games in this succinct formulation of cooperative games.
DEFF Research Database (Denmark)
Larsen, Peter Gorm; Lausdahl, Kenneth; Battle, Nick
2010-01-01
by forgotten preconditions as well as broken invariants and post-conditions. Trace definitions are defined as regular expressions describing possible sequences of operation calls, and are conceptually similar to UML sequence diagrams. In this paper we present a tool enabling test automation based on VDM traces......Abstract—Combinatorial testing in VDM involves the automatic generation and execution of a large collection of test cases derived from templates provided in the form of trace definitions added to a VDM specification. The main value of this is the rapid detection of run-time errors caused......, and explain how it is possible to reduce large collections of test cases in different ways. Its use is illustrated with a small case study....
Capturing Chemistry in Action with Electrons: Realization of Atomically Resolved Reaction Dynamics.
Ischenko, Anatoly A; Weber, Peter M; Miller, R J Dwayne
2017-08-23
One of the grand challenges in chemistry has been to directly observe atomic motions during chemical processes. The depiction of the nuclear configurations in space-time to understand barrier crossing events has served as a unifying intellectual theme connecting the different disciplines of chemistry. This challenge has been cast as an imaging problem in which the technical issues reduce to achieving not only sufficient simultaneous space-time resolution but also brightness for sufficient image contrast to capture the atomic motions. This objective has been met with electrons as the imaging source. The review chronicles the first use of electron structural probes to study reactive intermediates, to the development of high bunch charge electron pulses with sufficient combined spatial-temporal resolution and intensity to literally light up atomic motions, as well as the means to characterize the electron pulses in terms of temporal brightness and image reconstruction. The use of femtosecond Rydberg spectroscopy as a novel means to use internal electron scattering within the molecular reference frame to obtain similar information on reaction dynamics is also discussed. The focus is on atomically resolved chemical reaction dynamics with pertinent references to work in other areas and forms of spectroscopy that provide additional information. Effectively, we can now directly observe the far-from-equilibrium atomic motions involved in barrier crossing and categorize chemistry in terms of a power spectrum of a few dominant reaction modes. It is this reduction in dimensionality that makes chemical reaction mechanisms transferrable to seemingly arbitrarily complex (large N) systems, up to molecules as large as biological macromolecules (N > 1000 atoms). We now have a new way to reformulate reaction mechanisms using an experimentally determined dynamic mode basis that in combination with recent theoretical advances has the potential to lead to a new conceptual basis for
On an extension of a combinatorial identity
Indian Academy of Sciences (India)
to an infinite family of 4-way combinatorial identities. In some particular cases we get even 5-way combinatorial identities which give us four new combinatorial versions of. Göllnitz–Gordon identities. Keywords. n-Color partitions; lattice paths; Frobenius partitions; Göllnitz–Gordon identities; combinatorial interpretations. 1.
Antolini, Ermete
2017-02-13
Combinatorial chemistry and high-throughput screening represent an innovative and rapid tool to prepare and evaluate a large number of new materials, saving time and expense for research and development. Considering that the activity and selectivity of catalysts depend on complex kinetic phenomena, making their development largely empirical in practice, they are prime candidates for combinatorial discovery and optimization. This review presents an overview of recent results of combinatorial screening of low-temperature fuel cell electrocatalysts for methanol oxidation. Optimum catalyst compositions obtained by combinatorial screening were compared with those of bulk catalysts, and the effect of the library geometry on the screening of catalyst composition is highlighted.
Czech Academy of Sciences Publication Activity Database
Rech, C.; Rosencrantz, R. R.; Křenek, Karel; Pelantová, Helena; Bojarová, Pavla; Roemer, Ch. E.; Hanisch, F.-G.; Křen, Vladimír; Elling, L.
2011-01-01
Roč. 353, č. 13 (2011), s. 2492-2500 ISSN 1615-4150 R&D Projects: GA MŠk OC09045 Institutional research plan: CEZ:AV0Z50200510 Keywords : combinatorial chemistry * biocatalysis * carbohydrates Subject RIV: CC - Organic Chemistry Impact factor: 6.048, year: 2011
Energy Technology Data Exchange (ETDEWEB)
Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2015-02-14
The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.
Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M
2015-02-14
The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.
International Nuclear Information System (INIS)
Spicer, L.D.
1984-10-01
General areas of research addressed are recoil chemistry of halogens, tritium, and sulfur, radiotracer methods for studies of chemical dynamics, thermal and photochemistry of sulfur dioxide, and photochemistry and photoassistance in catalytic systems
Combinatorial designs constructions and analysis
Stinson, Douglas R
2004-01-01
Created to teach students many of the most important techniques used for constructing combinatorial designs, this is an ideal textbook for advanced undergraduate and graduate courses in combinatorial design theory. The text features clear explanations of basic designs, such as Steiner and Kirkman triple systems, mutual orthogonal Latin squares, finite projective and affine planes, and Steiner quadruple systems. In these settings, the student will master various construction techniques, both classic and modern, and will be well-prepared to construct a vast array of combinatorial designs. Design theory offers a progressive approach to the subject, with carefully ordered results. It begins with simple constructions that gradually increase in complexity. Each design has a construction that contains new ideas or that reinforces and builds upon similar ideas previously introduced. A new text/reference covering all apsects of modern combinatorial design theory. Graduates and professionals in computer science, applie...
Combinatorial Mathematics: Research into Practice
Sriraman, Bharath; English, Lyn D.
2004-01-01
Implications and suggestions for using combinatorial mathematics in the classroom through a survey and synthesis of numerous research studies are presented. The implications revolve around five major themes that emerge from analysis of these studies.
Combinatorial methods with computer applications
Gross, Jonathan L
2007-01-01
Combinatorial Methods with Computer Applications provides in-depth coverage of recurrences, generating functions, partitions, and permutations, along with some of the most interesting graph and network topics, design constructions, and finite geometries. Requiring only a foundation in discrete mathematics, it can serve as the textbook in a combinatorial methods course or in a combined graph theory and combinatorics course.After an introduction to combinatorics, the book explores six systematic approaches within a comprehensive framework: sequences, solving recurrences, evaluating summation exp
Number systems and combinatorial problems
Yordzhev, Krasimir
2014-01-01
The present work has been designed for students in secondary school and their teachers in mathematics. We will show how with the help of our knowledge of number systems we can solve problems from other fields of mathematics for example in combinatorial analysis and most of all when proving some combinatorial identities. To demonstrate discussed in this article method we have chosen several suitable mathematical tasks.
Relativity in Combinatorial Gravitational Fields
Directory of Open Access Journals (Sweden)
Mao Linfan
2010-04-01
Full Text Available A combinatorial spacetime $(mathscr{C}_G| uboverline{t}$ is a smoothly combinatorial manifold $mathscr{C}$ underlying a graph $G$ evolving on a time vector $overline{t}$. As we known, Einstein's general relativity is suitable for use only in one spacetime. What is its disguise in a combinatorial spacetime? Applying combinatorial Riemannian geometry enables us to present a combinatorial spacetime model for the Universe and suggest a generalized Einstein gravitational equation in such model. Forfinding its solutions, a generalized relativity principle, called projective principle is proposed, i.e., a physics law ina combinatorial spacetime is invariant under a projection on its a subspace and then a spherically symmetric multi-solutions ofgeneralized Einstein gravitational equations in vacuum or charged body are found. We also consider the geometrical structure in such solutions with physical formations, and conclude that an ultimate theory for the Universe maybe established if all such spacetimes in ${f R}^3$. Otherwise, our theory is only an approximate theory and endless forever.
Parameterization and evaluation of sulfate adsorption in a dynamic soil chemistry model
International Nuclear Information System (INIS)
Martinson, Liisa; Alveteg, Mattias; Warfvinge, Per
2003-01-01
Including sulfate adsorption improves the dynamic behavior of the SAFE model. - Sulfate adsorption was implemented in the dynamic, multi-layer soil chemistry model SAFE. The process is modeled by an isotherm in which sulfate adsorption is considered to be fully reversible and dependent on sulfate concentration as well as pH in soil solution. The isotherm was parameterized by a site-specific series of simple batch experiments at different pH (3.8-5.0) and sulfate concentration (10-260 μmol l -1 ) levels. Application of the model to the Lake Gaardsjoen roof covered site shows that including sulfate adsorption improves the dynamic behavior of the model and sulfate adsorption and desorption delay acidification and recovery of the soil. The modeled adsorbed pool of sulfate at the site reached a maximum level of 700 mmol/m 2 in the late 1980s, well in line with experimental data
Marin, Luminita; Ailincai, Daniela; Morariu, Simona; Tartau-Mititelu, Liliana
2017-08-15
The paper focusses on the synthesis of novel hydrogels by joining natural biodegradable compounds with the aim to achieve biocompatible materials for bio related applications. The hydrogels were prepared from chitosan and citral by constitutional dynamic chemistry, incorporating both molecular and supramolecular dynamic features. The hydrophobic flexible citral has been reversible immobilized onto the hydrophilic chitosan backbone via imine bonds to form amphiphilic glycodynamers, which further self-ordered through supramolecular interactions into a 3D-network of biodynameric hydrogel. The synthetic pathway has been demonstrated by NMR and FTIR spectroscopy, X-ray diffraction and polarized light microscopy. Studies of the hydrogel morphology revealed a 3D porous microstructure, whose pores size correlated with the crosslinking degree. Rheological investigations evidenced high elasticity, thermo-responsiveness and thixotropic behavior. As a proof of the concept, the hydrogels proved in vivo biocompatibility on laboratory mice. The paper successfully implements the constitutional dynamic chemistry in generation of chitosan high performance hydrogels. Copyright © 2017 Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
Ramesh K.
2018-01-01
Full Text Available The Rayleigh lidar at National Atmospheric Research Laboratory, Gadanki (13.5°N, 79.2°E, India operates at 532 nm green laser with ~600 mJ/pulse since 2007. The vertical temperature profiles are derived above ~30 km by assuming the atmosphere is in hydrostatic equilibrium and obeys ideal gas law. A large mesospheric inversion layer (MIL is observed at ~77.4-84.6 km on the night of 22 March 2007 over Gadanki. Although dynamics and chemistry play vital role, both the mechanisms are compared for the occurrence of the MIL in the present study.
Ramesh, K.; Sridharan, S.; Raghunath, K.
2018-04-01
The Rayleigh lidar at National Atmospheric Research Laboratory, Gadanki (13.5°N, 79.2°E), India operates at 532 nm green laser with 600 mJ/pulse since 2007. The vertical temperature profiles are derived above 30 km by assuming the atmosphere is in hydrostatic equilibrium and obeys ideal gas law. A large mesospheric inversion layer (MIL) is observed at 77.4-84.6 km on the night of 22 March 2007 over Gadanki. Although dynamics and chemistry play vital role, both the mechanisms are compared for the occurrence of the MIL in the present study.
International Nuclear Information System (INIS)
Kim, Dong Yeun; Kim, Oh Sik; Kim, Chang Guk; Park, Cheong Gil; Lee, Gwi Hyeon; Lee, Cheol Hui
1987-07-01
This book deals aquatic chemistry, which treats water and environment, chemical kinetics, chemical balance like dynamical characteristic, and thermodynamics, acid-base chemistry such as summary, definition, kinetics, and PH design for mixture of acid-base chemistry, complex chemistry with definition, and kinetics, precipitation and dissolution on summary, kinetics of precipitation and dissolution, and balance design oxidation and resolution with summary, balance of oxidation and resolution.
Combinatorial optimization theory and algorithms
Korte, Bernhard
2018-01-01
This comprehensive textbook on combinatorial optimization places special emphasis on theoretical results and algorithms with provably good performance, in contrast to heuristics. It is based on numerous courses on combinatorial optimization and specialized topics, mostly at graduate level. This book reviews the fundamentals, covers the classical topics (paths, flows, matching, matroids, NP-completeness, approximation algorithms) in detail, and proceeds to advanced and recent topics, some of which have not appeared in a textbook before. Throughout, it contains complete but concise proofs, and also provides numerous exercises and references. This sixth edition has again been updated, revised, and significantly extended. Among other additions, there are new sections on shallow-light trees, submodular function maximization, smoothed analysis of the knapsack problem, the (ln 4+ɛ)-approximation for Steiner trees, and the VPN theorem. Thus, this book continues to represent the state of the art of combinatorial opti...
Molecular dynamics for irradiation driven chemistry: application to the FEBID process*
Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.
2016-10-01
A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.
Spatiotemporal dynamics of spring and stream water chemistry in a high-mountain area
International Nuclear Information System (INIS)
Zelazny, Miroslaw; Astel, Aleksander; Wolanin, Anna; Malek, Stanislaw
2011-01-01
The present study deals with the application of the self-organizing map (SOM) technique in the exploration of spatiotemporal dynamics of spring and stream water samples collected in the Chocholowski Stream Basin located in the Tatra Mountains (Poland). The SOM-based classification helped to uncover relationships between physical and chemical parameters of water samples and factors determining the quality of water in the studied high-mountain area. In the upper part of the Chocholowski Stream Basin, located on the top of the crystalline core of the Tatras, concentrations of the majority of ionic substances were the lowest due to limited leaching. Significantly higher concentration of ionic substances was detected in spring and stream samples draining sedimentary rocks. The influence of karst-type springs on the quality of stream water was also demonstrated. - Highlights: → We use SOM approach to explore physiochemical data for mountain waters. → Geologic structure and hydrological events impact water chemistry. → Limited leaching, typical of crystalline core, reflects in low water mineralization. → Sedimentary rocks are susceptible for leaching. → Eutrophication has not been shown to be a threat in the Chocholowska Valley. - Spatiotemporal dynamics of spring and stream water chemistry in unique high-mountain area was evaluated by the self-organizing map technique.
Effect of the Implicit Combinatorial Model on Combinatorial Reasoning in Secondary School Pupils.
Batanero, Carmen; And Others
1997-01-01
Elementary combinatorial problems may be classified into three different combinatorial models: (1) selection; (2) partition; and (3) distribution. The main goal of this research was to determine the effect of the implicit combinatorial model on pupils' combinatorial reasoning before and after instruction. Gives an analysis of variance of the…
Lewellen, D. C.; Lewellen, W. S.
2001-01-01
High-resolution numerical large-eddy simulations of the near wake of a B757 including simplified NOx and HOx chemistry were performed to explore the effects of dynamics on chemistry in wakes of ages from a few seconds to several minutes. Dilution plays an important basic role in the NOx-O3 chemistry in the wake, while a more interesting interaction between the chemistry and dynamics occurs for the HOx species. These simulation results are compared with published measurements of OH and HO2 within a B757 wake under cruise conditions in the upper troposphere taken during the Subsonic Aircraft Contrail and Cloud Effects Special Study (SUCCESS) mission in May 1996. The simulation provides a much finer grained representation of the chemistry and dynamics of the early wake than is possible from the 1 s data samples taken in situ. The comparison suggests that the previously reported discrepancy of up to a factor of 20 - 50 between the SUCCESS measurements of the [HO2]/[OH] ratio and that predicted by simplified theoretical computations is due to the combined effects of large mixing rates around the wake plume edges and averaging over volumes containing large species fluctuations. The results demonstrate the feasibility of using three-dimensional unsteady large-eddy simulations with coupled chemistry to study such phenomena.
Label-free in situ imaging of oil body dynamics and chemistry in germination.
Waschatko, Gustav; Billecke, Nils; Schwendy, Sascha; Jaurich, Henriette; Bonn, Mischa; Vilgis, Thomas A; Parekh, Sapun H
2016-10-01
Plant oleosomes are uniquely emulsified lipid reservoirs that serve as the primary energy source during seed germination. These oil bodies undergo significant changes regarding their size, composition and structure during normal seedling development; however, a detailed characterization of these oil body dynamics, which critically affect oil body extractability and nutritional value, has remained challenging because of a limited ability to monitor oil body location and composition during germination in situ Here, we demonstrate via in situ, label-free imaging that oil bodies are highly dynamic intracellular organelles that are morphologically and biochemically remodelled extensively during germination. Label-free, coherent Raman microscopy (CRM) combined with bulk biochemical measurements revealed the temporal and spatial regulation of oil bodies in native soya bean cotyledons during the first eight days of germination. Oil bodies undergo a cycle of growth and shrinkage that is paralleled by lipid and protein compositional changes. Specifically, the total protein concentration associated with oil bodies increases in the first phase of germination and subsequently decreases. Lipids contained within the oil bodies change in saturation and chain length during germination. Our results show that CRM is a well-suited platform to monitor in situ lipid dynamics and local chemistry and that oil bodies are actively remodelled during germination. This underscores the dynamic role of lipid reservoirs in plant development. © 2016 The Authors.
Combinatorial optimization networks and matroids
Lawler, Eugene
2011-01-01
Perceptively written text examines optimization problems that can be formulated in terms of networks and algebraic structures called matroids. Chapters cover shortest paths, network flows, bipartite matching, nonbipartite matching, matroids and the greedy algorithm, matroid intersections, and the matroid parity problems. A suitable text or reference for courses in combinatorial computing and concrete computational complexity in departments of computer science and mathematics.
Algorithms in combinatorial design theory
Colbourn, CJ
1985-01-01
The scope of the volume includes all algorithmic and computational aspects of research on combinatorial designs. Algorithmic aspects include generation, isomorphism and analysis techniques - both heuristic methods used in practice, and the computational complexity of these operations. The scope within design theory includes all aspects of block designs, Latin squares and their variants, pairwise balanced designs and projective planes and related geometries.
Computational Complexity of Combinatorial Surfaces
Vegter, Gert; Yap, Chee K.
1990-01-01
We investigate the computational problems associated with combinatorial surfaces. Specifically, we present an algorithm (based on the Brahana-Dehn-Heegaard approach) for transforming the polygonal schema of a closed triangulated surface into its canonical form in O(n log n) time, where n is the
Combinatorial synthesis of ceramic materials
Lauf, Robert J.; Walls, Claudia A.; Boatner, Lynn A.
2006-11-14
A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.
Combinatorial auctions for electronic business
Indian Academy of Sciences (India)
R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22
(6) Information feedback: An auction protocol may be a direct mechanism or an .... transparency of allocation decisions arise in resolving these ties. .... bidding, however more recently, combinatorial bids are allowed [50] making ...... Also, truth revelation and other game theoretic considerations are not taken into account.
Combinatorial Proofs and Algebraic Proofs
Indian Academy of Sciences (India)
Permanent link: https://www.ias.ac.in/article/fulltext/reso/018/07/0630-0645. Keywords. Combinatorial proof; algebraic proof; binomial identity; recurrence relation; composition; Fibonacci number; Fibonacci identity; Pascal triangle. Author Affiliations. Shailesh A Shirali1. Sahyadri School Tiwai Hill, Rajgurunagar Pune 410 ...
Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation
Shiraiwa, Manabu; Yee, Lindsay D.; Schilling, Katherine A.; Loza, Christine L.; Craven, Jill S.; Zuend, Andreas; Ziemann, Paul J.; Seinfeld, John H.
2013-01-01
Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process. PMID:23818634
Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation.
Shiraiwa, Manabu; Yee, Lindsay D; Schilling, Katherine A; Loza, Christine L; Craven, Jill S; Zuend, Andreas; Ziemann, Paul J; Seinfeld, John H
2013-07-16
Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process.
Barbera, Jack
2007-12-01
This dissertation combines work in the areas of experimental physical chemistry and chemical education. In the area of physical chemistry, femtosecond pump-probe spectroscopy is used to interrogate the time-dependence for energy redistribution, solvent reorientation, and dissociation dynamics in small gas-phase anion clusters. The chemical education research addressed in this manuscript include the development and validation of a survey to measure students' beliefs about chemistry and the learning of chemistry and the development and testing of learning tutorials for use in undergraduate physical chemistry courses in thermodynamics and kinetics. In the first part of this dissertation, the Cu(CD3OD) dynamics are investigated using a combination of femtosecond pump-probe experiments and ab initio calculations. Dissociation of this complex into Cu and CD3OD occurs on two distinct time scales: 3 and 30 ps, which arise, respectively, from the coupling of intermolecular solvent rotations and excited methyl rotor rotation into the Cu-O dissociation component upon electron photodetachment of the precursor anion. In the second part of this dissertation, the time-resolved recombination of photodissociated IBr-(CO2)n (n = 5 - 10) cluster anions is investigated. Upon excitation to the A' 2pi 1/2 state of the chromophore, the bare anion results in I- and Br products, upon solvation with CO2, the IBr- chromophore regains near-IR absorption after recombination and vibrational relaxation on the ground electronic state. The recombination times vary with the number of solvent molecules from 12 ps for n = 5 to 900 ps for n = 10. Extensive electronic structure and non-adiabatic molecular dynamic simulations provide a framework to understand this behavior. In the third part of this dissertation, the modification and validation of the Colorado Learning Attitudes about Science Survey (CLASS) for use in chemistry is presented in detail. The CLASS survey is designed to measure student
Tuning the Electronic and Dynamical Properties of a Molecule by Atom Trapping Chemistry.
Pham, Van Dong; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie; Abad, Enrique; Dappe, Yannick J; Smogunov, Alexander; Lagoute, Jérôme
2017-11-28
The ability to trap adatoms with an organic molecule on a surface has been used to obtain a range of molecular functionalities controlled by the choice of the molecular trapping site and local deprotonation. The tetraphenylporphyrin molecule used in this study contains three types of trapping sites: two carbon rings (phenyl and pyrrole) and the center of a macrocycle. Catching a gold adatom on the carbon rings leads to an electronic doping of the molecule, whereas trapping the adatom at the macrocycle center with single deprotonation leads to a molecular rotor and a second deprotonation leads to a molecular jumper. We call "atom trapping chemistry" the control of the structure, electronic, and dynamical properties of a molecule achieved by trapping metallic atoms with a molecule on a surface. In addition to the examples previously described, we show that more complex structures can be envisaged.
Uhl, Bernd; Hirn, Stephanie; Mildner, Karina; Coletti, Raffaele; Massberg, Steffen; Reichel, Christoph A; Rehberg, Markus; Zeuschner, Dagmar; Krombach, Fritz
2018-03-01
To optimize the design of nanoparticles for diagnosis or therapy of vascular diseases, it is mandatory to characterize the determinants of nano-bio interactions in vascular lesions. Using ex vivo and in vivo microscopy, we analyzed the interactive behavior of quantum dots with different surface functionalizations in atherosclerotic lesions of ApoE-deficient mice. We demonstrate that quantum dots with different surface functionalizations exhibit specific interactive behaviors with distinct molecular and cellular components of the injured vessel wall. Moreover, we show a role for fibrinogen in the regulation of the spatio-temporal interaction dynamics in atherosclerotic lesions. Our findings emphasize the relevance of surface chemistry-driven nano-bio interactions on the differential in vivo behavior of nanoparticles in diseased tissue.
Upper atmosphere research satellite program. [to study the chemistry energetics, and dynamics
Huntress, W. T., Jr.
1978-01-01
A satellite program to conduct research on the chemistry, energetics, and dynamics of the upper atmosphere was developed. The scientific goals of the Upper Atmospheric Research Program, the program requirements, and the approach toward meeting those requirements are outlined. An initial series of two overlapping spacecraft missions is described. Both spacecraft are launched and recovered by the STS, one in the winter of 1983 at a 56 deg inclination, and the other a year later at a 70 deg inclination. The duration of each mission is 18 months, and each carries instruments to make global measurements of the temperature, winds, composition, irradation, and radiance in the stratosphere, mesosphere, and lower thermosphere between the tropopause and 120 km altitude. The program requires a dedicated ground-based data system and a science team organization that leads to a strong interaction between the experiments and theory. The program includes supportive observations from other platforms such as rockets, balloons, and the Spacelab.
Nguyen, Howard; Willacy, Karen; Allen, Mark
2012-01-01
KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.
Combinatorial Speculations and the Combinatorial Conjecture for Mathematics
Mao, Linfan
2006-01-01
Combinatorics is a powerful tool for dealing with relations among objectives mushroomed in the past century. However, an more important work for mathematician is to apply combinatorics to other mathematics and other sciences not merely to find combinatorial behavior for objectives. Recently, such research works appeared on journals for mathematics and theoretical physics on cosmos. The main purpose of this paper is to survey these thinking and ideas for mathematics and cosmological physics, s...
Pilarz, Matthew
2013-01-01
For this study, a research-based lab module was implemented in two high school chemistry classes for the purpose of examining classroom dynamics throughout the process of students completing the module. A research-based lab module developed for use in undergraduate laboratories by the Center for Authentic Science Practice in Education (CASPiE) was…
Combinatorial algebra syntax and semantics
Sapir, Mark V
2014-01-01
Combinatorial Algebra: Syntax and Semantics provides a comprehensive account of many areas of combinatorial algebra. It contains self-contained proofs of more than 20 fundamental results, both classical and modern. This includes Golod–Shafarevich and Olshanskii's solutions of Burnside problems, Shirshov's solution of Kurosh's problem for PI rings, Belov's solution of Specht's problem for varieties of rings, Grigorchuk's solution of Milnor's problem, Bass–Guivarc'h theorem about the growth of nilpotent groups, Kleiman's solution of Hanna Neumann's problem for varieties of groups, Adian's solution of von Neumann-Day's problem, Trahtman's solution of the road coloring problem of Adler, Goodwyn and Weiss. The book emphasize several ``universal" tools, such as trees, subshifts, uniformly recurrent words, diagrams and automata. With over 350 exercises at various levels of difficulty and with hints for the more difficult problems, this book can be used as a textbook, and aims to reach a wide and diversified...
Identification and Interrogation of Combinatorial Histone Modifications
Directory of Open Access Journals (Sweden)
Kelly R Karch
2013-12-01
Full Text Available Histone proteins are dynamically modified to mediate a variety of cellular processes including gene transcription, DNA damage repair, and apoptosis. Regulation of these processes occurs through the recruitment of non-histone proteins to chromatin by specific combinations of histone post-translational modifications (PTMs. Mass spectrometry has emerged as an essential tool to discover and quantify histone PTMs both within and between samples in an unbiased manner. Developments in mass spectrometry that allow for characterization of large histone peptides or intact protein has made it possible to determine which modifications occur simultaneously on a single histone polypeptide. A variety of techniques from biochemistry, biophysics, and chemical biology have been employed to determine the biological relevance of discovered combinatorial codes. This review first describes advancements in the field of mass spectrometry that have facilitated histone PTM analysis and then covers notable approaches to probe the biological relevance of these modifications in their nucleosomal context.
Combinatorial aspects of covering arrays
Directory of Open Access Journals (Sweden)
Charles J. Colbourn
2004-11-01
Full Text Available Covering arrays generalize orthogonal arrays by requiring that t -tuples be covered, but not requiring that the appearance of t -tuples be balanced.Their uses in screening experiments has found application in software testing, hardware testing, and a variety of fields in which interactions among factors are to be identified. Here a combinatorial view of covering arrays is adopted, encompassing basic bounds, direct constructions, recursive constructions, algorithmic methods, and applications.
Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai
2018-06-13
An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.
Lee, M L; Schneider, G
2001-01-01
Natural products were analyzed to determine whether they contain appealing novel scaffold architectures for potential use in combinatorial chemistry. Ring systems were extracted and clustered on the basis of structural similarity. Several such potential scaffolds for combinatorial chemistry were identified that are not present in current trade drugs. For one of these scaffolds a virtual combinatorial library was generated. Pharmacophoric properties of natural products, trade drugs, and the virtual combinatorial library were assessed using a self-organizing map. Obviously, current trade drugs and natural products have several topological pharmacophore patterns in common. These features can be systematically explored with selected combinatorial libraries based on a combination of natural product-derived and synthetic molecular building blocks.
Flamant, Cyrille
2017-04-01
The EU-funded project DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa, http://www.dacciwa.eu) is investigating the relationship between weather, climate and air pollution in southern West Africa. The air over the coastal region of West Africa is a unique mixture of natural and anthropogenic gases, liquids and particles, emitted in an environment, in which multi-layer cloud decks frequently form. These exert a large influence on the local weather and climate, mainly due to their impact on radiation, the surface energy balance and thus the diurnal cycle of the atmospheric boundary layer. The main objective for the aircraft detachment was to build robust statistics of cloud properties in southern West Africa in different chemical landscapes to investigate the physical processes involved in their life cycle in such a complex chemical environment. As part of the DACCIWA field campaigns, three European aircraft (the German DLR Falcon 20, the French SAFIRE ATR 42 and the British BAS Twin Otter) conducted a total of 50 research flights across Ivory Coast, Ghana, Togo, and Benin from 27 June to 16 July 2016 for a total of 155 flight hours, including hours sponsored through 3 EUFAR projects. The aircraft were used in different ways based on their strengths, but all three had comparable instrumentation with the the capability to do gas-phase chemistry, aerosol and clouds, thereby generating a rich dataset of atmospheric conditions across the region. Eight types of flight objectives were conducted to achieve the goals of the DACCIWA: (i) Stratus clouds, (ii) Land-sea breeze clouds, (iii) Mid-level clouds, (iv) Biogenic emission, (v) City emissions, (vi) Flaring and ship emissions, (vii) Dust and biomass burning aerosols, and (viii) air-sea interactions. An overview of the DACCIWA aircraft campaign as well as first highlights from the airborne observations will be presented.
Sakurai-Yageta, Mika; Maruyama, Tomoko; Suzuki, Takashi; Ichikawa, Kazuhisa; Murakami, Yoshinori
2015-01-01
Protein components of cell adhesion machinery show continuous renewal even in the static state of epithelial cells and participate in the formation and maintenance of normal epithelial architecture and tumor suppression. CADM1 is a tumor suppressor belonging to the immunoglobulin superfamily of cell adhesion molecule and forms a cell adhesion complex with an actin-binding protein, 4.1B, and a scaffold protein, MPP3, in the cytoplasm. Here, we investigate dynamic regulation of the CADM1-4.1B-MPP3 complex in mature cell adhesion by fluorescence recovery after photobleaching (FRAP) analysis. Traditional FRAP analysis were performed for relatively short period of around 10min. Here, thanks to recent advances in the sensitive laser detector systems, we examine FRAP of CADM1 complex for longer period of 60 min and analyze the recovery with exponential curve-fitting to distinguish the fractions with different diffusion constants. This approach reveals that the fluorescence recovery of CADM1 is fitted to a single exponential function with a time constant (τ) of approximately 16 min, whereas 4.1B and MPP3 are fitted to a double exponential function with two τs of approximately 40-60 sec and 16 min. The longer τ is similar to that of CADM1, suggesting that 4.1B and MPP3 have two distinct fractions, one forming a complex with CADM1 and the other present as a free pool. Fluorescence loss in photobleaching analysis supports the presence of a free pool of these proteins near the plasma membrane. Furthermore, double exponential fitting makes it possible to estimate the ratio of 4.1B and MPP3 present as a free pool and as a complex with CADM1 as approximately 3:2 and 3:1, respectively. Our analyses reveal a central role of CADM1 in stabilizing the complex with 4.1B and MPP3 and provide insight in the dynamics of adhesion complex formation. PMID:25780926
Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.
Kastrup, Christian J; Runyon, Matthew K; Lucchetta, Elena M; Price, Jessica M; Ismagilov, Rustem F
2008-04-01
Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to
Variational methods for direct/inverse problems of atmospheric dynamics and chemistry
Penenko, Vladimir; Penenko, Alexey; Tsvetova, Elena
2013-04-01
We present a variational approach for solving direct and inverse problems of atmospheric hydrodynamics and chemistry. It is important that the accurate matching of numerical schemes has to be provided in the chain of objects: direct/adjoint problems - sensitivity relations - inverse problems, including assimilation of all available measurement data. To solve the problems we have developed a new enhanced set of cost-effective algorithms. The matched description of the multi-scale processes is provided by a specific choice of the variational principle functionals for the whole set of integrated models. Then all functionals of variational principle are approximated in space and time by splitting and decomposition methods. Such approach allows us to separately consider, for example, the space-time problems of atmospheric chemistry in the frames of decomposition schemes for the integral identity sum analogs of the variational principle at each time step and in each of 3D finite-volumes. To enhance the realization efficiency, the set of chemical reactions is divided on the subsets related to the operators of production and destruction. Then the idea of the Euler's integrating factors is applied in the frames of the local adjoint problem technique [1]-[3]. The analytical solutions of such adjoint problems play the role of integrating factors for differential equations describing atmospheric chemistry. With their help, the system of differential equations is transformed to the equivalent system of integral equations. As a result we avoid the construction and inversion of preconditioning operators containing the Jacobi matrixes which arise in traditional implicit schemes for ODE solution. This is the main advantage of our schemes. At the same time step but on the different stages of the "global" splitting scheme, the system of atmospheric dynamic equations is solved. For convection - diffusion equations for all state functions in the integrated models we have developed the
First principles molecular dynamics insight into acid-base chemistry of clay minerals
International Nuclear Information System (INIS)
Liu, Xiandong; Lu, Xiancai; Wang, Rucheng; Meijer, Evert Jan
2012-01-01
Document available in extended abstract form only. Microscopic knowledge on the interfaces between clay minerals (2:1- and 1:1-type) and water is critical for both understanding natural processes and guiding development of advanced hybrid materials. Due to the unique layered structures of clay minerals, their surfaces are usually grouped into basal surfaces and edge surfaces (i.e. broken surfaces). Thanks to previous studies, structures and properties of basal surfaces have been well recognized: these surfaces are terminated with siloxanes and surface Si-O six-member rings normally act as the adsorbing sites of cations. In contrast, edge surfaces are more complicated structures and have more subtle chemical properties. On these surfaces, there are a lot of dangling bonds and under ambient conditions they are usually saturated by chemically adsorbed waters. These edge groups are usually amphoteric, which is responsible to the pH dependent behaviors of many interfacial processes, such as cations complexing. For example, adsorption of heavy metal cations (e.g. Ni 2+ , Co 2+ , Zn 2+ , Cd 2+ ) on clay basal surfaces is through cation exchange mechanism and that is hardly influenced by environmental pH. In contrast, it has been well accepted that the adsorption on edge surfaces is pH-dependent. The ubiquitous isomorphic substitutions further increase the complexity of their interfacial chemistry. Due to the high heterogeneity and rather small sizes, it is quite difficult to reveal the complex interfacial chemistry with experiments alone. FPMD method (first principles molecular dynamics), a combination of density functional theory and molecular dynamics, can provide valuable information. With FPMD [1, 2] and free-energy calculation techniques [3, 4], we investigated the microscopic structures and acid chemistry of these clay-water interfaces [5, 6]. According to systematic simulations, the following has been achieved. (1) Acidity of interlayer waters. The simulations show
International Nuclear Information System (INIS)
Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.
2012-01-01
We study the effect that non-equilibrium chemistry in dynamical models of collapsing molecular cloud cores has on measurements of the magnetic field in these cores, the degree of ionization, and the mean molecular weight of ions. We find that OH and CN, usually used in Zeeman observations of the line-of-sight magnetic field, have an abundance that decreases toward the center of the core much faster than the density increases. As a result, Zeeman observations tend to sample the outer layers of the core and consistently underestimate the core magnetic field. The degree of ionization follows a complicated dependence on the number density at central densities up to 10 5 cm –3 for magnetic models and 10 6 cm –3 in non-magnetic models. At higher central densities, the scaling approaches a power law with a slope of –0.6 and a normalization which depends on the cosmic-ray ionization rate ζ and the temperature T as (ζT) 1/2 . The mean molecular weight of ions is systematically lower than the usually assumed value of 20-30, and, at high densities, approaches a value of 3 due to the asymptotic dominance of the H + 3 ion. This significantly lower value implies that ambipolar diffusion operates faster.
Ozone budgets from the Dynamics and Chemistry of Marine Stratocumulus experiment
Kawa, S. R.; Pearson, R., Jr.
1989-01-01
Measurements from the Dynamics and Chemistry of marine Stratocumulus experiment have been used to study components of the regional ozone budget. The surface destruction rate is determined by eddy correlation of ozone and vertical velocity measured by a low-flying aircraft. Significant variability is found in the measured surface resistance; it is partially correlated with friction velocity but appears to have other controlling influences as well. The mean resistance is 4190 s/m which is higher (slower destruction) than most previous estimates for seawater. Flux and mean measurements throughout the marine boundary layer are used to estimate the net rate of in situ photochemical production/destruction of ozone. Averaged over the flights, ozone concentration is found to be near steady state, and a net of photochemical destruction of 0.02-0.07 ng/cu m per sec is diagnosed. This is an important confirmation of photochemical model results for the remote marine boundary layer. Ozone vertical distributions above the boundary layer show a strongly layered structure with very sharp gradients. These distributions are possibly related to the stratospheric ozone source.
Active Upper-atmosphere Chemistry and Dynamics from Polar Circulation Reversal on Titan
Teanby, Nicholas A.; Irwin, Patrick Gerard Joseph; Nixon, Conor A.; DeKok, Remco; Vinatier, Sandrine; Coustenis, Athena; Sefton-Nash, Elliot; Calcutt, Simon B.; Flasar, Michael F.
2012-01-01
Saturn's moon Titan has a nitrogen atmosphere comparable to Earth's, with a surface pressure of 1.4 bar. Numerical models reproduce the tropospheric conditions very well but have trouble explaining the observed middle-atmosphere temperatures, composition and winds. The top of the middle-atmosphere circulation has been thought to lie at an altitude of 450 to 500 kilometres, where there is a layer of haze that appears to be separated from the main haze deck. This 'detached' haze was previously explained as being due to the colocation of peak haze production and the limit of dynamical transport by the circulation's upper branch. Herewe report a build-up of trace gases over the south pole approximately two years after observing the 2009 post-equinox circulation reversal, from which we conclude that middle-atmosphere circulation must extend to an altitude of at least 600 kilometres. The primary drivers of this circulation are summer-hemisphere heating of haze by absorption of solar radiation and winter-hemisphere cooling due to infrared emission by haze and trace gases; our results therefore imply that these effects are important well into the thermosphere (altitudes higher than 500 kilometres). This requires both active upper-atmosphere chemistry, consistent with the detection of high-complexity molecules and ions at altitudes greater than 950 kilometres, and an alternative explanation for the detached haze, such as a transition in haze particle growth from monomers to fractal structures.
Kim, Kyung Lock; Park, Kyeng Min; Murray, James; Kim, Kimoon; Ryu, Sung Ho
2018-05-23
Combinatorial post-translational modifications (PTMs), which can serve as dynamic "molecular barcodes", have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways.
The Yoccoz Combinatorial Analytic Invariant
DEFF Research Database (Denmark)
Petersen, Carsten Lunde; Roesch, Pascale
2008-01-01
In this paper we develop a combinatorial analytic encoding of the Mandelbrot set M. The encoding is implicit in Yoccoz' proof of local connectivity of M at any Yoccoz parameter, i.e. any at most finitely renormalizable parameter for which all periodic orbits are repelling. Using this encoding we ...... to reprove that the dyadic veins of M are arcs and that more generally any two Yoccoz parameters are joined by a unique ruled (in the sense of Douady-Hubbard) arc in M....
Probabilistic methods in combinatorial analysis
Sachkov, Vladimir N
2014-01-01
This 1997 work explores the role of probabilistic methods for solving combinatorial problems. These methods not only provide the means of efficiently using such notions as characteristic and generating functions, the moment method and so on but also let us use the powerful technique of limit theorems. The basic objects under investigation are nonnegative matrices, partitions and mappings of finite sets, with special emphasis on permutations and graphs, and equivalence classes specified on sequences of finite length consisting of elements of partially ordered sets; these specify the probabilist
Log-balanced combinatorial sequences
Directory of Open Access Journals (Sweden)
Tomislav Došlic
2005-01-01
Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.
Ni, Cailing; Zha, Daijun; Ye, Hebo; Hai, Yu; Zhou, Yuntao; Anslyn, Eric V; You, Lei
2018-01-26
Axial chirality is a prevalent and important phenomenon in chemistry. Herein we report a combination of dynamic covalent chemistry and axial chirality for the development of a versatile platform for the binding and chirality sensing of multiple classes of mononucleophiles. An equilibrium between an open aldehyde and its cyclic hemiaminal within biphenyl derivatives enabled the dynamic incorporation of a broad range of alcohols, thiols, primary amines, and secondary amines with high efficiency. Selectivity toward different classes of nucleophiles was also achieved by regulating the distinct reactivity of the system with external stimuli. Through induced helicity as a result of central-to-axial chirality transfer, the handedness and ee values of chiral monoalcohol and monoamine analytes were reported by circular dichroism. The strategies introduced herein should find application in many contexts, including assembly, sensing, and labeling. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Combinatorial optimization on a Boltzmann machine
Korst, J.H.M.; Aarts, E.H.L.
1989-01-01
We discuss the problem of solving (approximately) combinatorial optimization problems on a Boltzmann machine. It is shown for a number of combinatorial optimization problems how they can be mapped directly onto a Boltzmann machine by choosing appropriate connection patterns and connection strengths.
Combinatorial Interpretation of General Eulerian Numbers
Tingyao Xiong; Jonathan I. Hall; Hung-Ping Tsao
2014-01-01
Since 1950s, mathematicians have successfully interpreted the traditional Eulerian numbers and $q-$Eulerian numbers combinatorially. In this paper, the authors give a combinatorial interpretation to the general Eulerian numbers defined on general arithmetic progressions { a, a+d, a+2d,...}.
Fourier analysis in combinatorial number theory
International Nuclear Information System (INIS)
Shkredov, Il'ya D
2010-01-01
In this survey applications of harmonic analysis to combinatorial number theory are considered. Discussion topics include classical problems of additive combinatorics, colouring problems, higher-order Fourier analysis, theorems about sets of large trigonometric sums, results on estimates for trigonometric sums over subgroups, and the connection between combinatorial and analytic number theory. Bibliography: 162 titles.
Fourier analysis in combinatorial number theory
Energy Technology Data Exchange (ETDEWEB)
Shkredov, Il' ya D [M. V. Lomonosov Moscow State University, Moscow (Russian Federation)
2010-09-16
In this survey applications of harmonic analysis to combinatorial number theory are considered. Discussion topics include classical problems of additive combinatorics, colouring problems, higher-order Fourier analysis, theorems about sets of large trigonometric sums, results on estimates for trigonometric sums over subgroups, and the connection between combinatorial and analytic number theory. Bibliography: 162 titles.
International Nuclear Information System (INIS)
Kalache, B; Novikova, T; Morral, A Fontcuberta i; Cabarrocas, P Roca i; Morscheidt, W; Hassouni, K
2004-01-01
We present the results of a study of a capacitively coupled hydrogen discharge by means of a one-dimensional numerical fluid model and experiments. The model includes a detailed description of the gas-phase chemistry taking into account the production of H - ions by dissociative attachment of H 2 vibrational levels. The population of these levels is described by a Boltzmann vibrational distribution function characterized by a vibrational temperature T V . The effect of the dissociative-attachment reaction on the discharge dynamics was investigated by varying the vibrational temperature, which was used as a model input parameter. Increasing the vibrational temperature from 1000 to 6000 K affects both the chemistry and the dynamics of the electrical discharge. Because of dissociative attachment, the H - ion density increases by seven orders of magnitude and the H - ion density to electron density ratio varies from 10 -7 to 6, while the positive ion density increases slightly. As a consequence, the atomic hydrogen density increases by a factor of three, and the sheath voltage drops from 95 to 75 V. Therefore, clear evidence of a strong coupling between chemistry and electrical dynamics through the production of H - ions is demonstrated. Moreover, satisfactory agreement between computed and measured values of atomic hydrogen and H - ion densities gives further support to the requirement of a detailed description of the hydrogen vibrational kinetics for capacitively coupled radio frequency discharge models in the Torr regime
International Nuclear Information System (INIS)
Fujiwara, Kazutoshi; Domae, Masafumi; Ohta, Joji; Yoneda, Kimitoshi; Inada, Fumio
2009-01-01
Flow Accelerated Corrosion (FAC), which is one of the important subjects at fossil and nuclear power plans, is caused by the accelerated dissolution of protective oxide film due to the turbulent flow. The influence factors on FAC such as water chemistry, material, and fluid dynamics are closely related to the oxide property so that the risk of FAC can be reduced by the suitable control of water chemistry. There are some FAC models and evaluation codes of FAC rate. Some of them are used in wall thinning management of nuclear power plant in some country. Nevertheless, these FAC codes include many empirical parameters so that some uncertainty to evaluate the synergistic effectiveness of factors are the controversial point for the application of FAC code to wall thinning management in Japanese nuclear power plant. In this study, a FAC model that can evaluate the effect of temperature, NH3 concentration, chromium content, and dissolved oxygen concentration on FAC rate was developed by considering the diffusion of dissolved species. The critical dissolved oxygen concentration, which can inhibit FAC, was also calculated by this model. (author)
Combinatorial constructions in ergodic theory and dynamics
Katok, Anatole
2003-01-01
Ergodic theory studies measure-preserving transformations of measure spaces. These objects are intrinsically infinite and the notion of an individual point or an orbit makes no sense. Still there is a variety of situations when a measure-preserving transformation (and its asymptotic behavior) can be well described as a limit of certain finite objects (periodic processes). In the first part of this book this idea is developed systematically, genericity of approximation in various categories is explored, and numerous applications are presented, including spectral multiplicity and properties of the maximal spectral type. The second part of the book contains a treatment of various constructions of cohomological nature with an emphasis on obtaining interesting asymptotic behavior from approximate pictures at different time scales. The book presents a view of ergodic theory not found in other expository sources and is suitable for graduate students familiar with measure theory and basic functional analysis.
Czech Academy of Sciences Publication Activity Database
Delcroix, Pauline; Pagliai, M.; Cardini, G.; Bégué, D.; Hanoune, B.
2015-01-01
Roč. 119, č. 38 (2015), s. 9785-9793 ISSN 1089-5639 Institutional support: RVO:61388963 Keywords : hydrogen bond dynamics * chemical equilibria * liquid water Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.883, year: 2015
Pawson, Steven; Lin, Shian-Jiann; Rood, Richard B.; Stajner, Ivanka; Nebuda, Sharon; Nielsen, J. Eric; Douglass, Anne R.
2000-01-01
In order to support the EOS-Chem project, a comprehensive assimilation package for the coupled chemical-dynamical system is being developed by the Data Assimilation Office at NASA GSFC. This involves development of a coupled chemistry/meteorology model and of data assimilation techniques for trace species and meteorology. The model is being developed using the flux-form semi-Lagrangian dynamical core of Lin and Rood, the physical parameterizations from the NCAR Community Climate Model, and atmospheric chemistry modules from the Atmospheric Chemistry and Dynamics branch at NASA GSFC. To date the following results have been obtained: (i) multi-annual simulations with the dynamics-radiation model show the credibility of the package for atmospheric simulations; (ii) initial simulations including a limited number of middle atmospheric trace gases reveal the realistic nature of transport mechanisms, although there is still a need for some improvements. Samples of these results will be shown. A meteorological assimilation system is currently being constructed using the model; this will form the basis for the proposed meteorological/chemical assimilation package. The latter part of the presentation will focus on areas targeted for development in the near and far terms, with the objective of Providing a comprehensive assimilation package for the EOS-Chem science experiment. The first stage will target ozone assimilation. The plans also encompass a reanalysis (ReSTS) for the 1991-1995 period, which includes the Mt. Pinatubo eruption and the time when a large number of UARS observations were available. One of the most challenging aspects of future developments will be to couple theoretical advances in tracer assimilation with the practical considerations of a real environment and eventually a near-real-time assimilation system.
Dorai, R
2003-01-01
Atmospheric pressure plasmas, and dielectric barrier discharges (DBDs) in particular, are being investigated for their use in the remediation of nitrogen oxides (NO sub x) from automotive exhausts. In their normal mode of operation, DBDs consist of a large density of short-lived filamentary microdischarges. Localized energy deposition results in spatially nonuniform gas temperatures and species densities which initiate advective and diffusive transport. Diesel exhausts, one of the major sources of NO sub x , typically contain unburned hydrocarbons (UHCs) which significantly influence the NO sub x chemistry during plasma remediation. In this paper, we discuss results from a computational investigation of the consequences of UHC chemistry on radial transport dynamics and remediation of NO sub x. In the presence of UHCs, radicals such as O and OH are dominantly consumed in the microstreamer region and their transport to larger radii is reduced. As a result, the conversion of NO to NO sub 2 is mainly restricted t...
The DACCIWA project: Dynamics-aerosol-chemistry-cloud interactions in West Africa
Knippertz, Peter
2017-04-01
This contribution provides an overview of the EU-funded DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa) project. DACCIWA consists of 16 European and African research organisations and has strong links to universities, weather services and government organisations across West Africa. The project runs from 2010 to 2018 and is built around a major international field campaign in 2016. A key motivation for DACCIWA is the expected tripling of anthropogenic emissions in southern West Africa (SWA) between 2000 and 2030, whose impacts on human health, ecosystems, food security and the regional climate are largely unknown. An integrated assessment of this problem, which is mostly due to massive economic and population growth and urbanization, is challenging due to (a) a superposition of regional effects with global climate change, (b) a strong dependence on the variable West African monsoon, (c) incomplete scientific understanding of interactions between emissions, clouds, radiation, precipitation and regional circulations, and (d) a lack of observations. DACCIWA combines measurements in the field in SWA with extensive modelling activities and work on satellite data. In particular during the main DACCIWA field campaign in June-July 2016 high-quality observations of emissions, atmospheric composition and meteorological parameters were sampled. The campaign involved three research aircraft, three ground-based supersites, enhanced radiosonde launches, and intensive measurements at urban sites in Abidjan and Cotonou. These data have already been quality-controlled and will be freely available to the research community through a database at http://baobab.sedoo.fr/DACCIWA/ after the end of the project. The resulting benchmark dataset is currently combined with a wide range of modelling and satellite-based research activities that will ultimately allow (a) an assessment of the roles of relevant physical, chemical and biological processes, (b) an improvement
Liousse, C.; Knippertz, P.; Flamant, C.; Adon, J.; Akpo, A.; Annesi-Maesano, I.; Assamoi, E.; Baeza, A.; Julien, B.; Bedou, M.; Brooks, B. J.; Chiu, J. Y. C.; Chiron, C.; Coe, H.; Danuor, S.; Djossou, J.; Evans, M. J.; Fayomi, B.; Fink, A. H.; Galy-Lacaux, C.; Gardrat, E.; Jegede, O.; Kalthoff, N.; Kedote, M.; Keita, S.; Kouame, K.; Konare, A.; Leon, J. F.; Mari, C. H.; Lohou, F.; Roblou, L.; Schlager, H.; Schwarzenboeck, A.; Toure, E. N.; Veronique, Y.
2016-12-01
The EU-funded project DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa) is investigating the relationship between weather, climate, air pollution and health in southern West Africa. The air over the coastal region of West Africa is a unique mixture of natural and anthropogenic gases, liquids and particles, emitted in an environment, in which multi-layer cloud decks frequently form. These exert a large influence on the local weather and climate, which has never been studied in detail over West Africa: this information is currently not included in the majority of weather and climate models. For the first time, the entire chain of impacts of natural and manmade emissions on the West African atmosphere was investigated in a coordinated field campaign. As part of this campaign, three research aircraft (Falcon 20, Twin Otter and ATR) based in Lomé (Togo) flew targeted 50 missions over West Africa from 27 June to 16 July 2016. In that campaign also, three highly instrumented measuring sites inland were set up with weather balloons launched several times a day across the region. The main objective was to build robust statistics of cloud properties in southern West Africa in different chemical landscapes (background state, ship/flaring emissions, polluted megacities, agricultural and forest areas, dust from the Sahel/Sahara). In addition, DACCIWA scientists working on measurements of urban emissions, air pollution, and health have set up four urban sites in Abidjan (Cote d'Ivoire) and Cotonou (Benin) focusing on main specific regional combustion sources (domestic fires, traffic and waste burning). Long-term measurements of gases and particles and census of hospital admissions for respiratory diseases were started in January 2015 and will continue until March 2017 to determine the links between human health and air pollution. Intensive measurement periods took place in July 2015, January 2016, and July 2016 (a final one is planned for January 2017) in
Tumor-targeting peptides from combinatorial libraries*
Liu, Ruiwu; Li, Xiaocen; Xiao, Wenwu; Lam, Kit S.
2018-01-01
Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges infighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors. PMID:27210583
Cubical version of combinatorial differential forms
DEFF Research Database (Denmark)
Kock, Anders
2010-01-01
The theory of combinatorial differential forms is usually presented in simplicial terms. We present here a cubical version; it depends on the possibility of forming affine combinations of mutual neighbour points in a manifold, in the context of synthetic differential geometry.......The theory of combinatorial differential forms is usually presented in simplicial terms. We present here a cubical version; it depends on the possibility of forming affine combinations of mutual neighbour points in a manifold, in the context of synthetic differential geometry....
Conferences on Combinatorial and Additive Number Theory
2014-01-01
This proceedings volume is based on papers presented at the Workshops on Combinatorial and Additive Number Theory (CANT), which were held at the Graduate Center of the City University of New York in 2011 and 2012. The goal of the workshops is to survey recent progress in combinatorial number theory and related parts of mathematics. The workshop attracts researchers and students who discuss the state-of-the-art, open problems, and future challenges in number theory.
Jack superpolynomials: physical and combinatorial definitions
International Nuclear Information System (INIS)
Desrosiers, P.; Mathieu, P.; Lapointe, L.
2004-01-01
Jack superpolynomials are eigenfunctions of the supersymmetric extension of the quantum trigonometric Calogero-Moser-Sutherland Hamiltonian. They are orthogonal with respect to the scalar product, dubbed physical, that is naturally induced by this quantum-mechanical problem. But Jack superpolynomials can also be defined more combinatorially, starting from the multiplicative bases of symmetric superpolynomials, enforcing orthogonality with respect to a one-parameter deformation of the combinatorial scalar product. Both constructions turn out to be equivalent. (author)
Combinatorial explosion in model gene networks
Edwards, R.; Glass, L.
2000-09-01
The explosive growth in knowledge of the genome of humans and other organisms leaves open the question of how the functioning of genes in interacting networks is coordinated for orderly activity. One approach to this problem is to study mathematical properties of abstract network models that capture the logical structures of gene networks. The principal issue is to understand how particular patterns of activity can result from particular network structures, and what types of behavior are possible. We study idealized models in which the logical structure of the network is explicitly represented by Boolean functions that can be represented by directed graphs on n-cubes, but which are continuous in time and described by differential equations, rather than being updated synchronously via a discrete clock. The equations are piecewise linear, which allows significant analysis and facilitates rapid integration along trajectories. We first give a combinatorial solution to the question of how many distinct logical structures exist for n-dimensional networks, showing that the number increases very rapidly with n. We then outline analytic methods that can be used to establish the existence, stability and periods of periodic orbits corresponding to particular cycles on the n-cube. We use these methods to confirm the existence of limit cycles discovered in a sample of a million randomly generated structures of networks of 4 genes. Even with only 4 genes, at least several hundred different patterns of stable periodic behavior are possible, many of them surprisingly complex. We discuss ways of further classifying these periodic behaviors, showing that small mutations (reversal of one or a few edges on the n-cube) need not destroy the stability of a limit cycle. Although these networks are very simple as models of gene networks, their mathematical transparency reveals relationships between structure and behavior, they suggest that the possibilities for orderly dynamics in such
Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.
2012-01-01
Background and purpose: Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers…
Herga, Nataša Rizman; Cagran, Branka; Dinevski, Dejan
2016-01-01
Understanding chemistry includes the ability to think on three levels: the macroscopic level, the symbolic level, and the level of particles--sub-microscopic level. Pupils have the most difficulty when trying to understand the sub-microscopic level because it is outside their range of experience. A virtual laboratory enables a simultaneous…
Matsumoto, Paul S.
2014-01-01
The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…
Supramolecular assembly/reassembly processes: molecular motors and dynamers operating at surfaces.
Ciesielski, Artur; Samorì, Paolo
2011-04-01
Among the many significant advances within the field of supramolecular chemistry over the past decades, the development of the so-called "dynamers" features a direct relevance to materials science. Defined as "combinatorial dynamic polymers", dynamers are constitutional dynamic systems and materials resulting from the application of the principles of supramolecular chemistry to polymer science. Like supramolecular materials in general, dynamers are reversible dynamic multifunctional architectures, capable of modifying their constitution by exchanging, recombining, incorporating components. They may exhibit a variety of novel properties and behave as adaptive materials. In this review we focus on the design of responsive switchable monolayers, i.e. monolayers capable to undergo significant changes in their physical or chemical properties as a result of external stimuli. Scanning tunneling microscopy studies provide direct evidence with a sub-nanometre resolution, on the formation and dynamic response of these self-assembled systems featuring controlled geometries and properties.
The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry
Directory of Open Access Journals (Sweden)
C. Adams
2013-01-01
Full Text Available In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO_{2} columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL in Eureka, Canada (80.05° N, 86.42° W using the differential optical absorption spectroscopy (DOAS technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI and Optical Spectrograph and Infra-Red Imager System (OSIRIS satellite measurements, Global Modeling Initiative (GMI simulations, and meteorological quantities. On 8 April 2011, NO_{2} columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO_{2} from NO. Additionally, GMI NO_{x} (NO + NO_{2} and N_{2}O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO_{2}. The anticyclone that transported lower-latitude NO_{x} above PEARL became frozen-in and persisted in dynamical and GMI N_{2}O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC in the middle stratosphere was lost due to reactions with the enhanced NO_{x}. Below the FrIAC (from the tropopause to 700 K, NO_{x} driven ozone loss above Eureka was larger than in previous years, according to GMI monthly average ozone loss rates. Using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS, ozone losses since 1 December 2010 were calculated at 600 K. In the air mass that was above Eureka on 20 May 2011, ozone losses reached 4.2 parts per million by
Grimme, Stefan; Bauer, Christopher Alexander
2015-01-01
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
Seasonal Dynamics in the Chemistry and Structure of the Fat Bodies of Bumblebee Queens
Czech Academy of Sciences Publication Activity Database
Votavová, A.; Tomčala, Aleš; Kofroňová, Edita; Kudzejová, Michaela; Šobotník, J.; Jiroš, Pavel; Komzáková, O.; Valterová, Irena
2015-01-01
Roč. 10, č. 11 (2015), e0142261/1-e0142261/14 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GA14-04291S Institutional support: RVO:61388963 Keywords : transmission electron microscopy * triacylglycerols * phospholipids * fat ty acid composition * glycogen Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.057, year: 2015 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142261
Dynamic vertical profiles of peat porewater chemistry in a northern peatland
Natalie A. Griffiths; Stephen D. Sebestyen
2016-01-01
We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0â3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large...
A Synthesis of Fluid Dynamics and Quantum Chemistry for the Design of Nanoelectronics
MacDougall, Preston J.
1998-01-01
In 1959, during a famous lecture entitled "There's Plenty of Room at the Bottom", Richard Feynman focused on the startling technical possibilities that would exist at the limit of miniaturization, that being atomically precise devices with dimensions in the nanometer range. A nanometer is both a convenient unit of length for medium to large sized molecules, and the root of the name of the new interdisciplinary field of "nanotechnology". Essentially, "nanoelectronics" denotes the goal of shrinking electronic devices, such as diodes and transistors, as well as integrated circuits of such devices that can perform logical operations, down to dimensions in the range of 100 nanometers. The thirty-year hiatus in the development of nanotechnology can figuratively be seen as a period of waiting for the bottom-up and atomically precise construction skills of synthetic chemistry to meet the top-down reductionist aspirations of device physics. The sub-nanometer domain of nineteenth-century classical chemistry has steadily grown, and state-of-the-art supramolecular chemistry can achieve atomic precision in non-repeating molecular assemblies of the size desired for nanotechnology. For nanoelectronics in particular, a basic understanding of the electron transport properties of molecules must also be developed. Quantum chemistry provides powerful computational methods that can accurately predict the properties of small to medium sized molecules on a desktop workstation, and those of large molecules if one has access to a supercomputer. Of the many properties of a molecule that quantum chemistry routinely predicts, the ability to carry a current is one that had not even been considered until recently. "Currently", there is a controversy over just how to define this key property. Reminiscent of the situation in high-Tc superconductivity, much of the difficulty arises from the different models that are used to simplify the complex electronic structure of real materials. A model
DPN-Generated Combinatorial Libraries
2012-02-29
µM final concentration) is added (Fig. 6). Control over deposition parameters was examined for two model proteins, cholera toxin β subunit (CTβ...conjugated anti- cholera toxin beta (anti-CTb). The wells in the mould are inverted pyramids with an average depth of 86 µm, edge length of 120 µm, and...Therapeutics,” (2011). 91. University of New Mexico , Chemistry Department Colloquium, Albuquerque, NM, “The Polyvalent Gold Nanoparticle Conjugate
International Nuclear Information System (INIS)
Ribnikar, S.; Anic, S.
1998-01-01
The proceedings has following chapters: Plenary lectures; Chemical Thermodynamics; Spectroscopy, Molecular Structures, Physical Chemistry of Plasma; Kinetics, Catalysis, Nonlinear Dynamics; Electrochemistry; Biophysical Chemistry, Photochemistry, Radiation Chemistry; Radiochemistry, Nuclear Chemistry; Solid State Physical Chemistry, Material Science; Macromolecular Physical Chemistry; Environmental Protection; Phase Boundaries; Complex Compounds; General Physical Chemistry. A separated abstract was prepared for each of the 20 papers selected from the three chapters: Biophysical Chemistry, Photochemistry, Radiation Chemistry; Radiochemistry, Nuclear Chemistry. and Environmental Protection. Refs and figs
Local formulae for combinatorial Pontryagin classes
International Nuclear Information System (INIS)
Gaifullin, Alexander A
2004-01-01
Let p(|K|) be the characteristic class of a combinatorial manifold K given by a polynomial p in the rational Pontryagin classes of K. We prove that for any polynomial p there is a function taking each combinatorial manifold K to a cycle z p (K) in its rational simplicial chains such that: 1) the Poincare dual of z p (K) represents the cohomology class p(|K|); 2) the coefficient of each simplex Δ in the cycle z p (K) is determined solely by the combinatorial type of linkΔ. We explicitly describe all such functions for the first Pontryagin class. We obtain estimates for the denominators of the coefficients of the simplices in the cycles z p (K)
A combinatorial wind field model
DEFF Research Database (Denmark)
Soleimanzadeh, Maryam; Wisniewski, Rafal; Sloth, Christoffer
2010-01-01
This report is the deliverable 2.4 in the project Distributed Control of Large-Scale Oshore Wind Farms with the acronym Aeolus. The objective of this deliverable is to provide an understanding of the wind eld model and dynamic variations superimposed on the mean eld. In this report a dynamical...
Kim, H.; Rempe, D. M.; Bishop, J. K.; Dietrich, W.; Fung, I.; Wood, T. J.
2012-12-01
average the water table remained elevated as subsequent rainstorms repeatedly recharged the system. Well10 solute concentration slowly increased at the end of the rainy season when the water table fell. In contrast, at the foot of the hill slope, even though the water table was responsive to each rainfall event, its water chemistry developed a strong dilution signatures only during the intense rainstorms (total rainfall > 70mm); the solute concentration decreased (e.g. [Mg] = 0.1mM) during the rising limb of the well hydrograph and recovered back to its pre-event value (e.g. [Mg] = 0.3mM) during the falling limb of the well hydrograph. During small storms, the solute concentration of Well 1 either did not change or slightly increased. Mid-slope showed similar behavior to Well 1. The Well 3 solute concentration was diluted about 3 fold (e.g. [Mg] 0.3mM to 0.1mM) as the water table rose and increased as the water table receded. However unlike Well 1, the water chemistry of Well 3 did not recover to its pre-event composition at any point during the rainy season and the recovery rate was slower than that of Well 1. These water chemistry observations provide insight into the dynamics of water movement within the fractured, weathered bedrock zone, and point to both vertical and lateral mixing processes that influence the chemical evolution of waters.
A quark interpretation of the combinatorial hierarchy
International Nuclear Information System (INIS)
Enqvist, Kari.
1979-01-01
We propose a physical interpretation of the second level of the combinatorial hierarchy in terms of three quarks, three antiquarks and the vacuum. This interpretation allows us to introduce a new quantum number, which measures electromagnetic mass splitting of the quarks. We extend our argument by analogue to baryons, and find some SU(3) and some new mass formulas for baryons. The generalization of our approach to other hierarchy levels is discussed. We present also an empirical mass formula for baryons, which seems to be loosely connected with the combinatorial hierarchy. (author)
Combinatorial designs a tribute to Haim Hanani
Hartman, A
1989-01-01
Haim Hanani pioneered the techniques for constructing designs and the theory of pairwise balanced designs, leading directly to Wilson''s Existence Theorem. He also led the way in the study of resolvable designs, covering and packing problems, latin squares, 3-designs and other combinatorial configurations.The Hanani volume is a collection of research and survey papers at the forefront of research in combinatorial design theory, including Professor Hanani''s own latest work on Balanced Incomplete Block Designs. Other areas covered include Steiner systems, finite geometries, quasigroups, and t-designs.
Estimating meme fitness in adaptive memetic algorithms for combinatorial problems.
Smith, J E
2012-01-01
Among the most promising and active research areas in heuristic optimisation is the field of adaptive memetic algorithms (AMAs). These gain much of their reported robustness by adapting the probability with which each of a set of local improvement operators is applied, according to an estimate of their current value to the search process. This paper addresses the issue of how the current value should be estimated. Assuming the estimate occurs over several applications of a meme, we consider whether the extreme or mean improvements should be used, and whether this aggregation should be global, or local to some part of the solution space. To investigate these issues, we use the well-established COMA framework that coevolves the specification of a population of memes (representing different local search algorithms) alongside a population of candidate solutions to the problem at hand. Two very different memetic algorithms are considered: the first using adaptive operator pursuit to adjust the probabilities of applying a fixed set of memes, and a second which applies genetic operators to dynamically adapt and create memes and their functional definitions. For the latter, especially on combinatorial problems, credit assignment mechanisms based on historical records, or on notions of landscape locality, will have limited application, and it is necessary to estimate the value of a meme via some form of sampling. The results on a set of binary encoded combinatorial problems show that both methods are very effective, and that for some problems it is necessary to use thousands of variables in order to tease apart the differences between different reward schemes. However, for both memetic algorithms, a significant pattern emerges that reward based on mean improvement is better than that based on extreme improvement. This contradicts recent findings from adapting the parameters of operators involved in global evolutionary search. The results also show that local reward schemes
Mansbach, Rachael A; Ferguson, Andrew L
2015-03-14
The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.
Energy Technology Data Exchange (ETDEWEB)
Shin, Young Jun; Kim, Yong Mo [Hanyang University, Seoul (Korea, Republic of)
2014-11-15
A two-dimensional model with the detailed chemistry and variable transport properties has been applied to numerically investigate the combustion processes and flame dynamics in the bilayer porous burner. To account for the velocity transition and diffusion influenced by solid matrix, porosity terms are included in the governing equations. Heat transfer coefficient is calculated by Nusselt number to reflect the effect of gas velocity, pore diameter, and material properties. The detailed chemistry is based on GRI 2.11. Numerical results indicate that the present approach is capable of the essential features of the premixed combustion in the porous media in terms of the precise flame structure, pollutant formation, and stabilization characteristics. In this bilayer porous burner, the heat transferred from the downstream flame zone is conducted to the upstream flame region through the solid matrix. This heat transfer process through the solid matrix substantially influences the flame structure and stabilization characteristics in the porous media. The predicted results are compared with experimental data in terms of temperature for gaseous mixture and solid matrix, CO and NO emission level. Based on numerical results, a precise comparison has been made for the freely propagating premixed flames and the premixed flames with a porous media for various inlet velocities.
Yegoshina, O. V.; Bolshakova, N. A.
2017-11-01
Organization of reliable chemical control for maintaining cycle chemistry is one of the most important problems to be solved at the present time the design and operation of thermal power plants. To maintain optimal parameters of cycle chemistry are used automated chemical control system and regulation system of dosing chemical reagents. Reliability and stability analyzer readings largely determine the reliability of the water cycle chemistry. Now the most common reagents are ammonia, alkali and film-forming amines. In this paper are presented the results of studies of the impact of concentration and composition of chemical reagents for readings stability of automatic analyzers and transients time of control systems for cycles chemistry. Research of the impact of chemical reagents on the dynamic behavior of regulation system for cycle chemistry was conducted at the experimental facility of the Department of thermal power stations of the Moscow Engineering Institute. This experimental facility is model of the work of regulation system for cycle chemistry close to the actual conditions on the energy facilities CHP. Analysis of results of the impact of chemical reagent on the dynamic behavior of ammonia and film forming amines dosing systems showed that the film-forming amines dosing system is more inertia. This emphasizes the transition process of the system, in which a half times longer dosing of ammonia. Results of the study can be used to improve the monitoring systems of water chemical treatment.
A New Approach for Proving or Generating Combinatorial Identities
Gonzalez, Luis
2010-01-01
A new method for proving, in an immediate way, many combinatorial identities is presented. The method is based on a simple recursive combinatorial formula involving n + 1 arbitrary real parameters. Moreover, this formula enables one not only to prove, but also generate many different combinatorial identities (not being required to know them "a…
Asessing for Structural Understanding in Childrens' Combinatorial Problem Solving.
English, Lyn
1999-01-01
Assesses children's structural understanding of combinatorial problems when presented in a variety of task situations. Provides an explanatory model of students' combinatorial understandings that informs teaching and assessment. Addresses several components of children's structural understanding of elementary combinatorial problems. (Contains 50…
International Nuclear Information System (INIS)
Padding, J T; Briels, W J
2011-01-01
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review current and past computer simulation techniques and critically assess their ability to provide such a link between chemistry and rheology. We distinguish between two classes of coarse-graining levels, which we term coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics (CGSD). In CGMD the coarse-grained beads are still relatively hard, thus automatically preventing bond crossing. This also implies an upper limit on the number of atoms that can be lumped together (up to five backbone carbon atoms) and therefore on the longest chain lengths that can be studied. To reach a higher degree of coarse-graining, in CGSD many more atoms are lumped together (more than ten backbone carbon atoms), leading to relatively soft beads. In that case friction and stochastic forces dominate the interactions, and action must be undertaken to prevent bond crossing. We also review alternative methods that make use of the tube model of polymer dynamics, by obtaining the entanglement characteristics through a primitive path analysis and by simulation of a primitive chain network. We finally review super-coarse-grained methods in which an entire polymer is represented by a single particle, and comment on ways to include memory effects and transient forces. (topical review)
Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.
Some aspects of metallic ion chemistry and dynamics in the mesosphere and thermosphere
Mathews, J. D.
1987-01-01
The relationship between the formation of sporadic layers of metallic ion and the dumping of these ions into the upper mesosphere is discussed in terms of the tidal wind, classical (i.e., windshear) and other more complex, perhaps highly nonlinear layer formation mechanisms, and a possible circulation mechanism for these ions. Optical, incoherent scatter radar, rocket, and satellite derived evidence for various layer formation mechanisms and for the metallic ion circulation system is reviewed. The results of simple one dimensional numerical model calculations of sporadic E and intermediate layer formation are presented along with suggestions for more advanced models of intense or blanketing sporadic E. The flux of metallic ions dumped by the tidal wind system into the mesosphere is estimated and compared with estimates of total particle flux of meteoric origin. Possible effects of the metallic ion flux and of meteoric dust on D region ion chemistry are discussed.
Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.
2012-07-01
Background and purpose : Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers require students to use approaches beyond direct application of LCP. Sample : The questionnaire was administered to 162 students studying their first year of advanced chemistry (age 16/17) in three high achieving London high schools. Design and methods : The students' explanations of reversible chemical systems were inductively coded to identify the explanatory approaches used and interviews with 13 students were used to check for consistency. AS level examination questions on reversible reactions were analysed to identify the types of explanations sought and the students' performance in these examinations was compared to questionnaire answers. Results : 19% of students used a holistic explanatory approach: when the rates of forward and reverse reactions are correctly described, recognising their simultaneous and mutually dependent nature. 36% used a mirrored reactions approach when the connected nature of the forward and reverse reactions is identified, but not their mutual dependency. 42% failed to recognize the interdependence of forward and reverse reactions (reactions not connected approach). Only 4% of marks for AS examination questions on reversible chemical systems asked for responses which went beyond either direct application of LCP or recall of equilibrium knowledge. 37% of students attained an A grade in their AS national examinations. Conclusions : Examinations favour the application of LCP making it possible to obtain the highest grade with little understanding of reversible chemical systems beyond a direct application of this algorithm. Therefore students' understanding may be attenuated so that they are
Kawa, S. R.; Bevilacqua, R.; Margitan, J. J.; Douglass, A. R.; Schoeberl, M. R.; Hoppel, K.; Sen, B.; Bhartia, P. K. (Technical Monitor)
2001-01-01
The morphology and evolution of the stratospheric ozone (O3) distribution at high latitudes in the Northern Hemisphere (NH) are examined for the late summer and fall seasons of 1999. This time period sets the O3 initial condition for the SOLVE/THESEO field mission performed during winter 1999-2000. In situ and satellite data are used along with a three-dimensional model of chemistry and transport (CTM) to determine the key processes that control the distribution of O3 in the lower-to-middle stratosphere. O3 in the vortex at the beginning of the winter season is found to be nearly constant from 500 to above 800 K with a value at 3 ppmv +/- approx. 10%. Values outside the vortex are up to a factor of 2 higher and increase significantly with potential temperature. The seasonal time series of data from POAM shows that relatively low O3 mixing ratios, which characterize the vortex in late fall, are already present at high latitudes at the end of summer before the vortex circulation sets up. Analysis of the CTM output shows that the minimum O3 and increase in variance in late summer are the result of: 1) stirring of polar concentric O3 gradients by nascent wave-driven transport, and 2) an acceleration of net photochemical loss with decreasing solar illumination. The segregation of low O3 mixing ratios into the vortex as the circulation strengthens through the fall suggests a possible feedback role between O3 chemistry and the vortex formation dynamics. Trajectory calculations from O3 sample points early in the fall, however, show only a weak correlation between initial O3 mixing ratio and potential vorticity later in the season consistent with order-of-magnitude calculations for the relative importance of O3 in the fall radiative balance at high latitudes. The possible connection between O3 chemistry and the dynamics of vortex formation does suggest that these feedbacks and sensitivities need to be better understood in order to make confident predictions of the recovery
Combinatorial biosynthesis of medicinal plant secondary metabolites
Julsing, Mattijs K.; Koulman, Albert; Woerdenbag, Herman J.; Quax, Wim J.; Kayser, Oliver
2006-01-01
Combinatorial biosynthesis is a new tool in the generation of novel natural products and for the production of rare and expensive natural products. The basic concept is combining metabolic pathways in different organisms on a genetic level. As a consequence heterologous organisms provide precursors
Infinitary Combinatory Reduction Systems: Normalising Reduction Strategies
Ketema, J.; Simonsen, Jakob Grue
2010-01-01
We study normalising reduction strategies for infinitary Combinatory Reduction Systems (iCRSs). We prove that all fair, outermost-fair, and needed-fair strategies are normalising for orthogonal, fully-extended iCRSs. These facts properly generalise a number of results on normalising strategies in
PIPERIDINE OLIGOMERS AND COMBINATORIAL LIBRARIES THEREOF
DEFF Research Database (Denmark)
1999-01-01
The present invention relates to piperidine oligomers, methods for the preparation of piperidine oligomers and compound libraries thereof, and the use of piperidine oligomers as drug substances. The present invention also relates to the use of combinatorial libraries of piperidine oligomers...... in libraries (arrays) of compounds especially suitable for screening purposes....
Gian-Carlos Rota and Combinatorial Math.
Kolata, Gina Bari
1979-01-01
Presents the first of a series of occasional articles about mathematics as seen through the eyes of its prominent scholars. In an interview with Gian-Carlos Rota of the Massachusetts Institute of Technology he discusses how combinatorial mathematics began as a field and its future. (HM)
A Model of Students' Combinatorial Thinking
Lockwood, Elise
2013-01-01
Combinatorial topics have become increasingly prevalent in K-12 and undergraduate curricula, yet research on combinatorics education indicates that students face difficulties when solving counting problems. The research community has not yet addressed students' ways of thinking at a level that facilitates deeper understanding of how students…
Torus actions, combinatorial topology, and homological algebra
International Nuclear Information System (INIS)
Bukhshtaber, V M; Panov, T E
2000-01-01
This paper is a survey of new results and open problems connected with fundamental combinatorial concepts, including polytopes, simplicial complexes, cubical complexes, and arrangements of subspaces. Attention is concentrated on simplicial and cubical subdivisions of manifolds, and especially on spheres. Important constructions are described that enable one to study these combinatorial objects by using commutative and homological algebra. The proposed approach to combinatorial problems is based on the theory of moment-angle complexes recently developed by the authors. The crucial construction assigns to each simplicial complex K with m vertices a T m -space Z K with special bigraded cellular decomposition. In the framework of this theory, well-known non-singular toric varieties arise as orbit spaces of maximally free actions of subtori on moment-angle complexes corresponding to simplicial spheres. It is shown that diverse invariants of simplicial complexes and related combinatorial-geometric objects can be expressed in terms of bigraded cohomology rings of the corresponding moment-angle complexes. Finally, it is shown that the new relationships between combinatorics, geometry, and topology lead to solutions of some well-known topological problems
Combinatorial Aspects of the Generalized Euler's Totient
Directory of Open Access Journals (Sweden)
Nittiya Pabhapote
2010-01-01
Full Text Available A generalized Euler's totient is defined as a Dirichlet convolution of a power function and a product of the Souriau-Hsu-Möbius function with a completely multiplicative function. Two combinatorial aspects of the generalized Euler's totient, namely, its connections to other totients and its relations with counting formulae, are investigated.
Quantum Resonance Approach to Combinatorial Optimization
Zak, Michail
1997-01-01
It is shown that quantum resonance can be used for combinatorial optimization. The advantage of the approach is in independence of the computing time upon the dimensionality of the problem. As an example, the solution to a constraint satisfaction problem of exponential complexity is demonstrated.
Logging to Facilitate Combinatorial System Testing
Kruse, P.M.; Prasetya, I.S.W.B.; Hage, J; Elyasov, Alexander
2014-01-01
Testing a web application is typically very complicated. Imposing simple coverage criteria such as function or line coverage is often not sufficient to uncover bugs due to incorrect components integration. Combinatorial testing can enforce a stronger criterion, while still allowing the
ON range searching in the group model and combinatorial discrepancy
DEFF Research Database (Denmark)
Larsen, Kasper Green
2014-01-01
In this paper we establish an intimate connection between dynamic range searching in the group model and combinatorial discrepancy. Our result states that, for a broad class of range searching data structures (including all known upper bounds), it must hold that $t_u t_q=\\Omega(\\mbox{disc}^2......)$, where $t_u$ is the worst case update time, $t_q$ is the worst case query time, and disc is the combinatorial discrepancy of the range searching problem in question. This relation immediately implies a whole range of exceptionally high and near-tight lower bounds for all of the basic range searching...... problems. We list a few of them in the following: (1) For $d$-dimensional halfspace range searching, we get a lower bound of $t_u t_q=\\Omega(n^{1-1/d})$. This comes within an lg lg $n$ factor of the best known upper bound. (2) For orthogonal range searching, we get a lower bound of $t_u t...
Czech Academy of Sciences Publication Activity Database
Šponer, Jiří
2009-01-01
Roč. 26, č. 6 (2009), s. 824-825 ISSN 0739-1102. [The 17th Conversation . 16.06.2009-20.06.2009, Albany] Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : molecular dynamics * RNA Subject RIV: BO - Biophysics
Hydrogels Based on Dynamic Covalent and Non Covalent Bonds: A Chemistry Perspective
Directory of Open Access Journals (Sweden)
Francesco Picchioni
2018-03-01
Full Text Available Hydrogels based on reversible covalent bonds represent an attractive topic for research at both academic and industrial level. While the concept of reversible covalent bonds dates back a few decades, novel developments continue to appear in the general research area of gels and especially hydrogels. The reversible character of the bonds, when translated at the general level of the polymeric network, allows reversible interaction with substrates as well as responsiveness to variety of external stimuli (e.g., self-healing. These represent crucial characteristics in applications such as drug delivery and, more generally, in the biomedical world. Furthermore, the several possible choices that can be made in terms of reversible interactions generate an almost endless number of possibilities in terms of final product structure and properties. In the present work, we aim at reviewing the latest developments in this field (i.e., the last five years by focusing on the chemistry of the systems at hand. As such, this should allow molecular designers to develop a toolbox for the synthesis of new systems with tailored properties for a given application.
International Nuclear Information System (INIS)
Rodgers, F.; Rodgers, M.A.
1987-01-01
The contents of this book include: Interaction of ionizing radiation with matter; Primary products in radiation chemistry; Theoretical aspects of radiation chemistry; Theories of the solvated electron; The radiation chemistry of gases; Radiation chemistry of colloidal aggregates; Radiation chemistry of the alkali halides; Radiation chemistry of polymers; Radiation chemistry of biopolymers; Radiation processing and sterilization; and Compound index
Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.
Yang, Qian; Sing-Long, Carlos A; Reed, Evan J
2017-08-01
We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.
Quantum fields and processes a combinatorial approach
Gough, John
2018-01-01
Wick ordering of creation and annihilation operators is of fundamental importance for computing averages and correlations in quantum field theory and, by extension, in the Hudson-Parthasarathy theory of quantum stochastic processes, quantum mechanics, stochastic processes, and probability. This book develops the unified combinatorial framework behind these examples, starting with the simplest mathematically, and working up to the Fock space setting for quantum fields. Emphasizing ideas from combinatorics such as the role of lattice of partitions for multiple stochastic integrals by Wallstrom-Rota and combinatorial species by Joyal, it presents insights coming from quantum probability. It also introduces a 'field calculus' which acts as a succinct alternative to standard Feynman diagrams and formulates quantum field theory (cumulant moments, Dyson-Schwinger equation, tree expansions, 1-particle irreducibility) in this language. Featuring many worked examples, the book is aimed at mathematical physicists, quant...
Gems of combinatorial optimization and graph algorithms
Skutella, Martin; Stiller, Sebastian; Wagner, Dorothea
2015-01-01
Are you looking for new lectures for your course on algorithms, combinatorial optimization, or algorithmic game theory? Maybe you need a convenient source of relevant, current topics for a graduate student or advanced undergraduate student seminar? Or perhaps you just want an enjoyable look at some beautiful mathematical and algorithmic results, ideas, proofs, concepts, and techniques in discrete mathematics and theoretical computer science? Gems of Combinatorial Optimization and Graph Algorithms is a handpicked collection of up-to-date articles, carefully prepared by a select group of international experts, who have contributed some of their most mathematically or algorithmically elegant ideas. Topics include longest tours and Steiner trees in geometric spaces, cartograms, resource buying games, congestion games, selfish routing, revenue equivalence and shortest paths, scheduling, linear structures in graphs, contraction hierarchies, budgeted matching problems, and motifs in networks. This ...
Quantum fields and processes a combinatorial approach
Gough, John
2018-01-01
Wick ordering of creation and annihilation operators is of fundamental importance for computing averages and correlations in quantum field theory and, by extension, in the Hudson–Parthasarathy theory of quantum stochastic processes, quantum mechanics, stochastic processes, and probability. This book develops the unified combinatorial framework behind these examples, starting with the simplest mathematically, and working up to the Fock space setting for quantum fields. Emphasizing ideas from combinatorics such as the role of lattice of partitions for multiple stochastic integrals by Wallstrom–Rota and combinatorial species by Joyal, it presents insights coming from quantum probability. It also introduces a 'field calculus' which acts as a succinct alternative to standard Feynman diagrams and formulates quantum field theory (cumulant moments, Dyson–Schwinger equation, tree expansions, 1-particle irreducibility) in this language. Featuring many worked examples, the book is aimed at mathematical physicists,...
Three Syntactic Theories for Combinatory Graph Reduction
DEFF Research Database (Denmark)
Danvy, Olivier; Zerny, Ian
2011-01-01
in a third syntactic theory. The structure of the store-based abstract machine corresponding to this third syntactic theory oincides with that of Turner's original reduction machine. The three syntactic theories presented here The three syntactic heories presented here therefore have the following......We present a purely syntactic theory of graph reduction for the canonical combinators S, K, and I, where graph vertices are represented with evaluation contexts and let expressions. We express this syntactic theory as a reduction semantics, which we refocus into the first storeless abstract machine...... for combinatory graph reduction, which we refunctionalize into the first storeless natural semantics for combinatory graph reduction.We then factor out the introduction of let expressions to denote as many graph vertices as possible upfront instead of on demand, resulting in a second syntactic theory, this one...
Three Syntactic Theories for Combinatory Graph Reduction
DEFF Research Database (Denmark)
Danvy, Olivier; Zerny, Ian
2013-01-01
, as a store-based reduction semantics of combinatory term graphs. We then refocus this store-based reduction semantics into a store-based abstract machine. The architecture of this store-based abstract machine coincides with that of Turner's original reduction machine. The three syntactic theories presented......We present a purely syntactic theory of graph reduction for the canonical combinators S, K, and I, where graph vertices are represented with evaluation contexts and let expressions. We express this rst syntactic theory as a storeless reduction semantics of combinatory terms. We then factor out...... the introduction of let expressions to denote as many graph vertices as possible upfront instead of on demand . The factored terms can be interpreted as term graphs in the sense of Barendregt et al. We express this second syntactic theory, which we prove equivalent to the rst, as a storeless reduction semantics...
Exploiting Quantum Resonance to Solve Combinatorial Problems
Zak, Michail; Fijany, Amir
2006-01-01
Quantum resonance would be exploited in a proposed quantum-computing approach to the solution of combinatorial optimization problems. In quantum computing in general, one takes advantage of the fact that an algorithm cannot be decoupled from the physical effects available to implement it. Prior approaches to quantum computing have involved exploitation of only a subset of known quantum physical effects, notably including parallelism and entanglement, but not including resonance. In the proposed approach, one would utilize the combinatorial properties of tensor-product decomposability of unitary evolution of many-particle quantum systems for physically simulating solutions to NP-complete problems (a class of problems that are intractable with respect to classical methods of computation). In this approach, reinforcement and selection of a desired solution would be executed by means of quantum resonance. Classes of NP-complete problems that are important in practice and could be solved by the proposed approach include planning, scheduling, search, and optimal design.
Plume and wake dynamics, mixing, and chemistry behind an HSCT aircraft
Miake-Lye, R. C.; Martinez-Sanchez, M.; Brown, R. C.; Kolb, C. E.
1991-01-01
The chemical evolution and mixing and vortical motion of a High Speed Civil Transport's engine exhausts must be analyzed in order to track the gas and its speciation as emissions are mixed to atmospheric scales. Attention is presently given to an analytic model of the wake dynamical processes which accounts for the roll-up of the trailing vorticity, its breakup due to the Crow instability, and the subsequent evolution and motion of the reconnected vorticity. The concentrated vorticity is noted to wrap up the buoyant exhaust and suppress its continued mixing and dilution. The species tracked encompass those which could be heterogeneously reactive on the surfaces of the condensed ice particles, and those capable of reacting with exhaust soot particle surfaces to form active contrail and/or cloud condensation nuclei.
Combinatorial Cis-regulation in Saccharomyces Species
Directory of Open Access Journals (Sweden)
Aaron T. Spivak
2016-03-01
Full Text Available Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1 chromatin immunoprecipitation data for colocalization of transcription factors, (2 gene expression data for coexpression of predicted regulatory targets, and (3 gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1 combinatorial cis-regulation can be inferred by multi-genome analysis and (2 combinatorial cis-regulation can explain differences in gene expression between species.
The Combinatorial Trace Method in Action
Krebs, Mike; Martinez, Natalie C.
2013-01-01
On any finite graph, the number of closed walks of length k is equal to the sum of the kth powers of the eigenvalues of any adjacency matrix. This simple observation is the basis for the combinatorial trace method, wherein we attempt to count (or bound) the number of closed walks of a given length so as to obtain information about the graph's…
Crow, S.; Cooper, E.; Beilman, D.; Filley, T.; Reimer, P.
2009-04-01
On the Svalbard archipelago, as in other high Arctic regions, tundra soil organic matter (SOM) is primarily plant detritus that is largely stabilized by cold, moist conditions and low nitrogen availability. However, the resistance of SOM to decomposition is also influenced by the quality of organic matter inputs to soil. Different plant communities are likely to give different qualities to SOM, especially where lignin-rich woody species encroach into otherwise graminoid and bryophyte-dominated regions. Arctic woody plant species are particularly sensitive to changes in temperature, snow cover, and growing season length. In a changing environment, litter chemistry may emerge as an important control on tundra SOM stabilization. In summer 2007, we collected plant material and soil from the highly-organic upper horizon (appx. 0-5 cm) and the mineral-dominated lower horizon (appx. 5-10cm) from four locations in the southwest facing valleys of Svalbard, Norway. The central goal of the ongoing experiment is to determine whether a greater abundance of woody plants could provide a negative feedback to warming impacts on the carbon (C) balance of Arctic soils. Towards this, we used a combination of plant biopolymer analyses (cupric oxide oxidation and quantification of lignin-derived phenols and cutin/suberin-derived aliphatics) and radiocarbon-based estimates of C longevity and mean residence time (MRT) to characterize potential links between plant type and soil C pools. We found that graminoid species regenerate above- and belowground tissue each year, whereas woody species (Cassiope tetragona and Dryas octopetala) regenerated only leaves yearly. In contrast, C within live branches and roots persisted for 15-18 yr on average. Leaves from woody species remained nearly intact in surface litter for up to 20 yr without being incorporated into the upper soil horizon. Leaves from both graminoid and woody species were concentrated in lignin-derived phenols relative to roots, but
Dynamic High Pressure Study of Chemistry and Physics of Molecular Materials
Jezowski, Sebastian Ryszard
Both temperature and pressure control and influence the packing of molecules in crystalline phases. Our molecular simulations indicate that at ambient pressure, the cubic polymorph of tetracyanoethylene, TCNE, is the energetically stable form up to ˜ 160 K. The observed transition from the cubic to the monoclinic polymorph occurs however only at temperatures above ˜ 318 K due to the large transition barrier. The temperature-induced phase transition in TCNE studied with high-resolution IR spectroscopy is explained in terms of the increased vibrational entropy in the crystals of the monoclinic polymorph. Based upon the inverted design of the Merril-Bassett Diamond Anvil Cell, an improved, second generation dynamic Diamond Anvil Cell was developed. Based on the fluorescence of ruby crystals, we were able to demonstrate that the pressure variation range can be further increased at least up to 7 kbar and that the dynamic pressure compression of up to 1400 GPa/s can be achieved. A new class of mechanophoric system, bis-anthracene, BA, and its photoisomer, PI, is shown to respond reversibly to a mild, static pressure induced by a Diamond Anvil Cell as well as to shear deformation based on absorption spectroscopic measurements. The forward reaction occurs upon illumination with light while the back-reaction may be accelerated upon heating or mechanical stress, coupled to a rehybridization on four equivalent carbon atoms. It is an intriguing result as high pressure stabilizes the photodimerized species in related systems. Our molecular volume simulations ruled out significant differences in the volumes between bis-anthracene and its photoisomer. Kinetic absorption measurements at several different pressures reveal a negative volume of activation in the exothermic back-reaction at room temperature. Through a series of temperature-dependent kinetic measurements it is shown that the barrier of activation for the back-reaction is reduced by more than an order of magnitude at
Ghobadi, Ahmadreza F; Jayaraman, Arthi
2016-02-28
In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.
Jabeen, Nyla; Maqbool, Qaisar; Bibi, Tahira; Nazar, Mudassar; Hussain, Syed Z; Hussain, Talib; Jan, Tariq; Ahmad, Ishaq; Maaza, Malik; Anwaar, Sadaf
2018-06-01
Mounting-up economic losses to annual crops yield due to micronutrient deficiency, fertiliser inefficiency and increasing microbial invasions (e.g. Xanthomonas cempestri attack on tomatoes) are needed to be solved via nano-biotechnology. So keeping this in view, the authors' current study presents the new horizon in the field of nano-fertiliser with highly nutritive and preservative effect of green fabricated zinc oxide-nanostructures (ZnO-NSs) during Lycopersicum esculentum (tomato) growth dynamics. ZnO-NS prepared via green chemistry possesses highly homogenous crystalline structures well-characterised through ultraviolet and visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction and scanning electron microscope. The ZnO-NS average size was found as small as 18 nm having a crystallite size of 5 nm. L. esculentum were grown in different concentrations of ZnO-NS to examine the different morphological parameters includes time of seed germination, germination percentage, the number of plant leaves, the height of the plant, average number of branches, days count for flowering and fruiting time period along with fruit quantity. Promising results clearly predict that bio-fabricated ZnO-NS at optimum concentration resulted as growth booster and dramatically triggered the plant yield.
Two is better than one; toward a rational design of combinatorial therapy.
Chen, Sheng-Hong; Lahav, Galit
2016-12-01
Drug combination is an appealing strategy for combating the heterogeneity of tumors and evolution of drug resistance. However, the rationale underlying combinatorial therapy is often not well established due to lack of understandings of the specific pathways responding to the drugs, and their temporal dynamics following each treatment. Here we present several emerging trends in harnessing properties of biological systems for the optimal design of drug combinations, including the type of drugs, specific concentration, sequence of addition and the temporal schedule of treatments. We highlight recent studies showing different approaches for efficient design of drug combinations including single-cell signaling dynamics, adaption and pathway crosstalk. Finally, we discuss novel and feasible approaches that can facilitate the optimal design of combinatorial therapy. Copyright © 2016 Elsevier Ltd. All rights reserved.
Venus O2 visible and IR nightglow: Implications for lower thermosphere dynamics and chemistry
Bougher, S. W.; Borucki, W. J.
1994-01-01
The National Center for Atmospheric Research thermospheric general circulation model for the Venus thermosphere is modified to examine two observed night airglow features, both of which serve as sensitive tracers of the thermospheric circulation. New O2 nightglow data from the Pioneer Venus Orbiter (PVO) star tracker (O2 Herzberg II at 400-800 nm) and ground-based telescopes (O2 IR at 1.27 microns) yield additional model constraints for estimating Venus winds over 100-130 km. Atomic oxygen, produced by dayside CO2 photolysis peaking near 110 km, and transported to the nightside by the global wind system, is partially destroyed through three-body recombination, yielding the O2 Herzberg II visible nightglow. This emission is very sensitive to horizontal winds at altitudes between 100 and 130 km. Other trace species catalytic reactions also contribute to the production of the very strong nightside infrared (1.27 microns) emission. This paper examines the dynamical and chemical implications of these new data using the Venus thermospheric general circulation model (VTGCM) as an analysis tool. Three-dimensional calculations are presented for both solar maximum and solar medium conditions, corresponding to early PVO (1979-1981) and PVO entry (mid-1992) time periods. Very distinct periods are identified in which zonal winds are alternately weak and strong in the Venus lower thermosphere. VTGCM sensitivity studies are conducted to assess the impacts of potential changes in thermospheric zonal and day-to-night winds, and eddy diffusion on the corresponding nightglow intensities. It appears that cyclostrophic balance extends above 80 km periodically, owing to a reversal of the upper mesosphere latitudinal temperature gradient, and thereby producing strong zonal winds and correspondingly modified O2 nightglow distributions that are observed.
Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ.
Hofbauer, Stefan; Dalla Sega, Marco; Scheiblbrandner, Stefan; Jandova, Zuzana; Schaffner, Irene; Mlynek, Georg; Djinović-Carugo, Kristina; Battistuzzi, Gianantonio; Furtmüller, Paul G; Oostenbrink, Chris; Obinger, Christian
2016-09-27
Recently, a novel pathway for heme b biosynthesis in Gram-positive bacteria has been proposed. The final poorly understood step is catalyzed by an enzyme called HemQ and includes two decarboxylation reactions leading from coproheme to heme b. Coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. In the study presented here, we focus on HemQs from Listeria monocytogenes (LmHemQ) and Staphylococcus aureus (SaHemQ) recombinantly produced as apoproteins in Escherichia coli. We demonstrate the rapid and two-phase uptake of coproheme by both apo forms and the significant differences in thermal stability of the apo forms, coproheme-HemQ and heme b-HemQ. Reduction of ferric high-spin coproheme-HemQ to the ferrous form is shown to be enthalpically favored but entropically disfavored with standard reduction potentials of -205 ± 3 mV for LmHemQ and -207 ± 3 mV for SaHemQ versus the standard hydrogen electrode at pH 7.0. Redox thermodynamics suggests the presence of a pronounced H-bonding network and restricted solvent mobility in the heme cavity. Binding of cyanide to the sixth coproheme position is monophasic but relatively slow (∼1 × 10(4) M(-1) s(-1)). On the basis of the available structures of apo-HemQ and modeling of both loaded forms, molecular dynamics simulation allowed analysis of the interaction of coproheme and heme b with the protein as well as the role of the flexibility at the proximal heme cavity and the substrate access channel for coproheme binding and heme b release. Obtained data are discussed with respect to the proposed function of HemQ in monoderm bacteria.
MIFT: GIFT Combinatorial Geometry Input to VCS Code
1977-03-01
r-w w-^ H ^ß0318is CQ BRL °RCUMr REPORT NO. 1967 —-S: ... MIFT: GIFT COMBINATORIAL GEOMETRY INPUT TO VCS CODE Albert E...TITLE (and Subtitle) MIFT: GIFT Combinatorial Geometry Input to VCS Code S. TYPE OF REPORT & PERIOD COVERED FINAL 6. PERFORMING ORG. REPORT NUMBER...Vehicle Code System (VCS) called MORSE was modified to accept the GIFT combinatorial geometry package. GIFT , as opposed to the geometry package
North, K. P.; Mackay, D. M.; Scow, K. M.
2010-12-01
In situ bioremediation has typically been confirmed by collecting sediment and groundwater samples to directly demonstrate a degradation process in a laboratory microcosm. However, recent advances in molecular biological tools present options for demonstrating degradation processes with field-based tools that are less time-consuming. We have been investigating the capability of some of these molecular biological tools to evaluate in situ biodegradation of tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), and benzene at two field sites in California. At both sites, we have deployed Bio-Traps® (“traps”), made of Bio-Sep® beads in slotted PVC pipe, which provide ideal environments for microbial colonization. Stable Isotope Probing can be accomplished by sorbing the13C-labeled organic contaminant of concern onto Bio-Sep® beads (“baiting”); incorporation of 13C into the biomass collected by the trap would indicate that the microbial community was capable of degrading the labeled compound. In addition, we examined the chemistry and flow dynamics of these traps and present those results here. We performed a field experiment and a lab experiment to, in part, define the rate that different baits leached off various traps. At a TBA- and MTBE-contaminated site at Vandenberg AFB, Lompoc, CA, the TBA-dominant plume was effectively treated by recirculation/oxygenation of groundwater, decreasing TBA and MTBE concentrations to detection limits along predicted flowpaths created by two pairs of recirculation wells. We used the generated aerobic treatment zone to deploy traps baited with 13C-labeled MTBE or TBA in a novel, ex situ experimental setup. The groundwater flow extracted from the aerobic treatment zone was split through several chambers, each containing a trap and monitoring of influent and effluent. The chamber effluent was measured throughout a six-week deployment and analyzed for both TBA and MTBE; the majority of mass leached from the baited traps did
Advanced Aqueous Phase Catalyst Development using Combinatorial Methods, Phase II
National Aeronautics and Space Administration — Combinatorial methods are proposed to develop advanced Aqueous Oxidation Catalysts (AOCs) with the capability to mineralize organic contaminants present in effluents...
Particulate matter chemistry and dynamics in the twilight zone at VERTIGO ALOHA and K2 sites
Bishop, James K. B.; Wood, T. J.
2008-12-01
Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERtical Transport In the Global Ocean (VERTIGO) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by ˜100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting 3 weeks, contrasted oligotrophic station ALOHA (22.75°N 158°W), sampled in June-July 2004, with a biologically productive location (47 °N 161°E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C org, N, P, Ca, Si, Sr, Ba, Mn) in 51 μm size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C org and C-Star particle beam attenuation coefficient ( C P) were consistently related at both sites with a 27 μM m -1 conversion factor. At K2, C P profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed ˜40% and 10%, night and day, respectively to >51 μm C org of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 μm C org, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 μm Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO 4 precipitating Acantharia. Notable at K2 were major changes in water column inventories of many particulate components to 700 m over 10 days
Particulate matter chemistry and dynamics in the Twilight Zone at VERTIGO ALOHA and K2 Sites
Energy Technology Data Exchange (ETDEWEB)
Bishop, James K.B.; Wood, T.J.
2008-03-25
Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERTIGO (VERtical Transformations In the Global Ocean) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by {approx}100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting three weeks, contrasted oligotrophic station ALOHA (22.75{sup o}N 158{sup o}W), sampled in June-July 2004, with a biologically productive location (47{sup o}N 161{sup o}E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C{sub org}, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 {micro}m size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C{sub org} and C-Star particle beam attenuation coefficient (C{sub P}) were consistently related at both sites with a 27 {micro}M m{sup -1} conversion factor. 26 At K2, C{sub P} profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed {approx}40% and 10%, night and day, respectively to >51 {micro}m C{sub org} of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 {micro}m C{sub org}, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 {micro}m Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO{sub 4
"One-sample concept" micro-combinatory for high throughput TEM of binary films.
Sáfrán, György
2018-04-01
Phases of thin films may remarkably differ from that of bulk. Unlike to the comprehensive data files of Binary Phase Diagrams [1] available for bulk, complete phase maps for thin binary layers do not exist. This is due to both the diverse metastable, non-equilibrium or instable phases feasible in thin films and the required volume of characterization work with analytical techniques like TEM, SAED and EDS. The aim of the present work was to develop a method that remarkably facilitates the TEM study of the diverse binary phases of thin films, or the creation of phase maps. A micro-combinatorial method was worked out that enables both preparation and study of a gradient two-component film within a single TEM specimen. For a demonstration of the technique thin Mn x Al 1- x binary samples with evolving concentration from x = 0 to x = 1 have been prepared so that the transition from pure Mn to pure Al covers a 1.5 mm long track within the 3 mm diameter TEM grid. The proposed method enables the preparation and study of thin combinatorial samples including all feasible phases as a function of composition or other deposition parameters. Contrary to known "combinatorial chemistry", in which a series of different samples are deposited in one run, and investigated, one at a time, the present micro-combinatorial method produces a single specimen condensing a complete library of a binary system that can be studied, efficiently, within a single TEM session. That provides extremely high throughput for TEM characterization of composition-dependent phases, exploration of new materials, or the construction of phase diagrams of binary films. Copyright © 2018 Elsevier B.V. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Cousin, F
2004-09-01
After most pollution studies independently devoted to gases and aerosols, there now appears an urgent need to consider their interactions. In this view, an aerosol module has been implemented in the Meso-NH-C model to simulate two IOPs documented during the ESCOMPTE campaign which took place in the Marseille/Fos-Berre region in June-July 2001. First, modelled dynamic parameters (winds, temperatures, boundary layer thickness) and gaseous chemistry have been validated with measurements issued from the exhaustive ESCOMPTE database. Sensitivity analysis have also been performed using different gaseous emission inventories at various resolution. These simulations have illustrated the deep impact of both synoptic and local dynamics on observed ozone concentrations on June 24 (IOP2b) in the ESCOMPTE domain. Afterwards, the ORISAM aerosol module has been introduced into the Meso-NH-C model. Dynamics, gaseous chemistry and aerosol processes have thus been coupled on-line. The particulate pollution episode on June 24 (IOP2b) has been characterised through a satisfactory comparison, specially from sub-micron particles, between modelling and measurements at different representative stations in the domain. This study, with validation of the particulate emission inventory has also highlighted the need for future improvements, such as further characterisation of organic and inorganic aerosol species and consideration of coarse particles. Aerosol impact on gaseous chemistry has been preliminary approached in view of future development and modification to be given to the Meso-NH-C model. (author)
Effects of Suboptimal Bidding in Combinatorial Auctions
Schneider, Stefan; Shabalin, Pasha; Bichler, Martin
Though the VCG auction assumes a central place in the mechanism design literature, there are a number of reasons for favoring iterative combinatorial auction designs. Several promising ascending auction formats have been developed throughout the past few years based on primal-dual and subgradient algorithms and linear programming theory. Prices are interpreted as a feasible dual solution and the provisional allocation is interpreted as a feasible primal solution. iBundle( 3) (Parkes and Ungar 2000), dVSV (de Vries et al. 2007) and the Ascending Proxy auction (Ausubel and Milgrom 2002) result in VCG payoffs when the coalitional value function satisfies the buyer submodularity condition and bidders bid straightforward, which is an expost Nash equilibrium in that case. iBEA and CreditDebit auctions (Mishra and Parkes 2007) do not even require the buyer submodularity condition and achieve the same properties for general valuations. In many situations, however, one cannot assume bidders to bid straightforward and it is not clear from the theory how these non-linear personalized price auctions (NLPPAs) perform in this case. Robustness of auctions with respect to different bidding behavior is therefore a critical issue for any application. We have conducted a large number of computational experiments to analyze the performance of NLPPA designs with respect to different bidding strategies and different valuation models. We compare the results of NLPPAs to those of the VCG auction and those of iterative combinatorial auctions with approximate linear prices, such as ALPS (Bichler et al. 2009) and the Combinatorial Clock auction (Porter et al. 2003).
Recursive deconvolution of combinatorial chemical libraries.
Erb, E; Janda, K D; Brenner, S
1994-01-01
A recursive strategy that solves for the active members of a chemical library is presented. A pentapeptide library with an alphabet of Gly, Leu, Phe, and Tyr (1024 members) was constructed on a solid support by the method of split synthesis. One member of this library (NH2-Tyr-Gly-Gly-Phe-Leu) is a native binder to a beta-endorphin antibody. A variation of the split synthesis approach is used to build the combinatorial library. In four vials, a member of the library's alphabet is coupled to a...
Quantum resonance for simulating combinatorial problems
International Nuclear Information System (INIS)
Zak, Michail; Fijany, Amir
2005-01-01
Quantum computing by simulations is based upon similarity between mathematical formalism of a quantum phenomenon and phenomena to be analyzed. In this Letter, the mathematical formalism of quantum resonance combined with tensor product decomposability of unitary evolutions is mapped onto a class of NP-complete combinatorial problems. It has been demonstrated that nature has polynomial resources for solving NP-complete problems and that will help to develop a new strategy for artificial intelligence, as well as to re-evaluate the role of natural selection in biological evolution
Automatic generation of combinatorial test data
Zhang, Jian; Ma, Feifei
2014-01-01
This book reviews the state-of-the-art in combinatorial testing, with particular emphasis on the automatic generation of test data. It describes the most commonly used approaches in this area - including algebraic construction, greedy methods, evolutionary computation, constraint solving and optimization - and explains major algorithms with examples. In addition, the book lists a number of test generation tools, as well as benchmarks and applications. Addressing a multidisciplinary topic, it will be of particular interest to researchers and professionals in the areas of software testing, combi
On Definitions and Existence of Combinatorial Entropy of 2d Fields
DEFF Research Database (Denmark)
Forchhammer, Søren Otto; Shtarkov, Yuri; Justesen, Jørn
1998-01-01
Different definitions of combinatorial entropy is presented and conditions for their existence examined.......Different definitions of combinatorial entropy is presented and conditions for their existence examined....
Combinatorial Quantum Field Theory and Gluing Formula for Determinants
Reshetikhin, N.; Vertman, B.
2015-01-01
We define the combinatorial Dirichlet-to-Neumann operator and establish a gluing formula for determinants of discrete Laplacians using a combinatorial Gaussian quantum field theory. In case of a diagonal inner product on cochains we provide an explicit local expression for the discrete
Combinatorial Libraries of Bis-Heterocyclic Compounds with Skeletal Diversity
Soural, Miroslav; Bouillon, Isabelle; Krchňák, Viktor
2009-01-01
Combinatorial solid-phase synthesis of bis-heterocyclic compounds, characterized by the presence of two heterocyclic cores connected by a spacer of variable length/structure, provided structurally heterogeneous libraries with skeletal diversity. Both heterocyclic rings were assembled on resin in a combinatorial fashion. PMID:18811208
Combinatorial Libraries of Bis-Heterocyclic Compounds with Skeletal Diversity
Soural, Miroslav; Bouillon, Isabelle; Krchňák, Viktor
2008-01-01
Combinatorial solid-phase synthesis of bis-heterocyclic compounds, characterized by the presence of two heterocyclic cores connected by a spacer of variable length/structure, provided structurally heterogeneous libraries with skeletal diversity. Both heterocyclic rings were assembled on resin in a combinatorial fashion.
Combinatorial identities for tenth order mock theta functions
Indian Academy of Sciences (India)
44
which lead us to one 4-way and one 3-way combinatorial identity. ... mock theta functions, partition identities and different combinatorial parameters, see for ... 3. Example 1.1. There are twelve (n + 1)–color partitions of 2: 21, 21 + 01, 11 + 11, ...
Directory of Open Access Journals (Sweden)
Jenny Rivers
Full Text Available Immobilized combinatorial peptide libraries have been advocated as a strategy for equalization of the dynamic range of a typical proteome. The technology has been applied predominantly to blood plasma and other biological fluids such as urine, but has not been used extensively to address the issue of dynamic range in tissue samples. Here, we have applied the combinatorial library approach to the equalization of a tissue where there is also a dramatic asymmetry in the range of abundances of proteins; namely, the soluble fraction of skeletal muscle. We have applied QconCAT and label-free methodology to the quantification of the proteins that bind to the beads as the loading is progressively increased. Although some equalization is achieved, and the most abundant proteins no longer dominate the proteome analysis, at high protein loadings a new asymmetry of protein expression is reached, consistent with the formation of complex assembles of heat shock proteins, cytoskeletal elements and other proteins on the beads. Loading at different ionic strength values leads to capture of different subpopulations of proteins, but does not completely eliminate the bias in protein accumulation. These assemblies may impair the broader utility of combinatorial library approaches to the equalization of tissue proteomes. However, the asymmetry in equalization is manifest at either low and high ionic strength values but manipulation of the solvent conditions may extend the capacity of the method.
Energy Technology Data Exchange (ETDEWEB)
Brown, N.J. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
This research is concerned with the development and use of sensitivity analysis tools to probe the response of dependent variables to model input variables. Sensitivity analysis is important at all levels of combustion modeling. This group`s research continues to be focused on elucidating the interrelationship between features in the underlying potential energy surface (obtained from ab initio quantum chemistry calculations) and their responses in the quantum dynamics, e.g., reactive transition probabilities, cross sections, and thermal rate coefficients. The goals of this research are: (i) to provide feedback information to quantum chemists in their potential surface refinement efforts, and (ii) to gain a better understanding of how various regions in the potential influence the dynamics. These investigations are carried out with the methodology of quantum functional sensitivity analysis (QFSA).
Exact model reduction of combinatorial reaction networks
Directory of Open Access Journals (Sweden)
Fey Dirk
2008-08-01
Full Text Available Abstract Background Receptors and scaffold proteins usually possess a high number of distinct binding domains inducing the formation of large multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species grows exponentially with the number of binding domains and can easily reach several millions. Even by including only a limited number of components and binding domains the resulting models are very large and hardly manageable. A novel model reduction technique allows the significant reduction and modularization of these models. Results We introduce methods that extend and complete the already introduced approach. For instance, we provide techniques to handle the formation of multi-scaffold complexes as well as receptor dimerization. Furthermore, we discuss a new modeling approach that allows the direct generation of exactly reduced model structures. The developed methods are used to reduce a model of EGF and insulin receptor crosstalk comprising 5,182 ordinary differential equations (ODEs to a model with 87 ODEs. Conclusion The methods, presented in this contribution, significantly enhance the available methods to exactly reduce models of combinatorial reaction networks.
Chemistry of natural products: A veritable approach to the ...
African Journals Online (AJOL)
Even with the advent of newer technologies such as combinatorial chemistry, robotics, high throughput screening (HTS), bioinformatics, and in silico molecular modelling, natural products still play a crucial role in drug discovery. This is because they provide an unparalleled range of chemical diversity on which the newer ...
chemistry of marketed plants of eastern and southern africa
African Journals Online (AJOL)
More recently combinatorial chemistry and high throughout robotic screening techniques have been employed mostly by the big multinational pharmaceutical companies. Each one of these approaches has it benefits and disadvantages and the selection depends upon the goals of the project and the resources available to ...
Petsko, Gregory A
2004-01-01
General chemistry courses haven't changed significantly in forty years. Because most basic chemistry students are premedical students, medical schools have enormous influence and could help us start all over again to create undergraduate chemistry education that works.
Spatially Resolved Artificial Chemistry
DEFF Research Database (Denmark)
Fellermann, Harold
2009-01-01
Although spatial structures can play a crucial role in chemical systems and can drastically alter the outcome of reactions, the traditional framework of artificial chemistry is a well-stirred tank reactor with no spatial representation in mind. Advanced method development in physical chemistry has...... made a class of models accessible to the realms of artificial chemistry that represent reacting molecules in a coarse-grained fashion in continuous space. This chapter introduces the mathematical models of Brownian dynamics (BD) and dissipative particle dynamics (DPD) for molecular motion and reaction...
Spatially Resolved Artificial Chemistry
DEFF Research Database (Denmark)
Fellermann, Harold
2009-01-01
made a class of models accessible to the realms of artificial chemistry that represent reacting molecules in a coarse-grained fashion in continuous space. This chapter introduces the mathematical models of Brownian dynamics (BD) and dissipative particle dynamics (DPD) for molecular motion and reaction......Although spatial structures can play a crucial role in chemical systems and can drastically alter the outcome of reactions, the traditional framework of artificial chemistry is a well-stirred tank reactor with no spatial representation in mind. Advanced method development in physical chemistry has...
Energy Technology Data Exchange (ETDEWEB)
Chu, Young Hwan [Department of New Energy.Resource Engineering, College of Science and Engineering, Sangji University, 124, Sangjidae-gil, Wonju-si, Gangwon-Do 220-702 (Korea); Shul, Yong Gun [Department of Chemical and Biomolecular Engineering, Yonsei University, 134, Shinchon-Dong, Seodaemun-Gu, Seoul 120-749 (Korea)
2010-10-15
Low-temperature direct alcohol fuel cells fed with different kinds of alcohol (methanol, ethanol and 2-propanol) have been investigated by employing ternary electrocatalysts (Pt-Ru-Sn) as anode catalysts. Combinatorial chemistry has been applied to screen the 66-PtRuSn-anode arrays at the same time to reduce cost, time, and effort when we select the optimum composition of electrocatalysts for DAFCs (Direct Alcohol Fuel Cells). PtRuSn (80:20:0) showed the lowest onset potential for methanol electro-oxidation, PtRuSn (50:0:50) for ethanol, and PtRuSn (20:70:10) for 2-propanol in CV results respectively, and single cell performance test indicated that Ru is more suitable for direct methanol fuel cell system, Sn for direct ethanol fuel cell system, and 2-propanol could be applied as fuel with low platinum composition anode electrocatalyst. The single cell performance results and electrochemical results (CV) were well matched with the combinatorial electrochemical results. As a result, we could verify the availability of combinatorial chemistry by comparing the results of each extreme electrocatalysts compositions as follows: PtRuSn (80:20:0) for methanol, PtRuSn (50:0:50) for ethanol and PtRuSn (20:70:10) for 2-propanol. (author)
Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad
2015-02-15
The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported. © 2014 Wiley Periodicals, Inc.
Zhong, Jian; Cai, Xiao-Ming; Bloss, William James
2017-05-01
A large eddy simulation (LES) model coupled with O 3 -NO x -VOC chemistry is implemented to simulate the coupled effects of emissions, mixing and chemical pre-processing within an idealised deep (aspect ratio = 2) urban street canyon under a weak wind condition. Reactive pollutants exhibit significant spatial variations in the presence of two vertically aligned unsteady vortices formed in the canyon. Comparison of the LES results from two chemical schemes (simple NO x -O 3 chemistry and a more comprehensive Reduced Chemical Scheme (RCS) chemical mechanism) shows that the concentrations of NO 2 and O x inside the street canyon are enhanced by approximately 30-40% via OH/HO 2 chemistry. NO, NO x , O 3 , OH and HO 2 are chemically consumed, while NO 2 and O x (total oxidant) are chemically produced within the canyon environment. Within-canyon pre-processing increases oxidant fluxes from the canyon to the overlying boundary layer, and this effect is greater for deeper street canyons (as found in many traditional European urban centres) than shallower (lower aspect ratio) streets. There is clear evidence of distinct behaviours for emitted chemical species and entrained chemical species, and positive (or negative) values of intensities of segregations are found between pairs of species with similar (or opposite) behaviour. The simplified two-box model underestimated NO and O 3 levels, but overestimated NO 2 levels for both the lower and upper canyon compared with the more realistic LES-chemistry model. This suggests that the segregation effect due to incomplete mixing reduces the chemical conversion rate of NO to NO 2 . This study reveals the impacts of nonlinear O 3 -NO x -VOC photochemical processes in the incomplete mixing environment and provides a better understanding of the pre-processing of emissions within canyons, prior to their release to the urban boundary layer, through the coupling of street canyon dynamics and chemistry. Copyright © 2017 Elsevier Ltd
Bifurcation-based approach reveals synergism and optimal combinatorial perturbation.
Liu, Yanwei; Li, Shanshan; Liu, Zengrong; Wang, Ruiqi
2016-06-01
Cells accomplish the process of fate decisions and form terminal lineages through a series of binary choices in which cells switch stable states from one branch to another as the interacting strengths of regulatory factors continuously vary. Various combinatorial effects may occur because almost all regulatory processes are managed in a combinatorial fashion. Combinatorial regulation is crucial for cell fate decisions because it may effectively integrate many different signaling pathways to meet the higher regulation demand during cell development. However, whether the contribution of combinatorial regulation to the state transition is better than that of a single one and if so, what the optimal combination strategy is, seem to be significant issue from the point of view of both biology and mathematics. Using the approaches of combinatorial perturbations and bifurcation analysis, we provide a general framework for the quantitative analysis of synergism in molecular networks. Different from the known methods, the bifurcation-based approach depends only on stable state responses to stimuli because the state transition induced by combinatorial perturbations occurs between stable states. More importantly, an optimal combinatorial perturbation strategy can be determined by investigating the relationship between the bifurcation curve of a synergistic perturbation pair and the level set of a specific objective function. The approach is applied to two models, i.e., a theoretical multistable decision model and a biologically realistic CREB model, to show its validity, although the approach holds for a general class of biological systems.
Characterizing the combinatorial beam angle selection problem
Bangert, Mark; Ziegenhein, Peter; Oelfke, Uwe
2012-10-01
The beam angle selection (BAS) problem in intensity-modulated radiation therapy is often interpreted as a combinatorial optimization problem, i.e. finding the best combination of η beams in a discrete set of candidate beams. It is well established that the combinatorial BAS problem may be solved efficiently with metaheuristics such as simulated annealing or genetic algorithms. However, the underlying parameters of the optimization process, such as the inclusion of non-coplanar candidate beams, the angular resolution in the space of candidate beams, and the number of evaluated beam ensembles as well as the relative performance of different metaheuristics have not yet been systematically investigated. We study these open questions in a meta-analysis of four strategies for combinatorial optimization in order to provide a reference for future research related to the BAS problem in intensity-modulated radiation therapy treatment planning. We introduce a high-performance inverse planning engine for BAS. It performs a full fluence optimization for ≈3600 treatment plans per hour while handling up to 50 GB of dose influence data (≈1400 candidate beams). For three head and neck patients, we compare the relative performance of a genetic, a cross-entropy, a simulated annealing and a naive iterative algorithm. The selection of ensembles with 5, 7, 9 and 11 beams considering either only coplanar or all feasible candidate beams is studied for an angular resolution of 5°, 10°, 15° and 20° in the space of candidate beams. The impact of different convergence criteria is investigated in comparison to a fixed termination after the evaluation of 10 000 beam ensembles. In total, our simulations comprise a full fluence optimization for about 3000 000 treatment plans. All four combinatorial BAS strategies yield significant improvements of the objective function value and of the corresponding dose distributions compared to standard beam configurations with equi
Combinatorial nanomedicines for colon cancer therapy.
Anitha, A; Maya, S; Sivaram, Amal J; Mony, U; Jayakumar, R
2016-01-01
Colon cancer is one of the major causes of cancer deaths worldwide. Even after surgical resection and aggressive chemotherapy, 50% of colorectal carcinoma patients develop recurrent disease. Thus, the rationale of developing new therapeutic approaches to improve the current chemotherapeutic regimen would be highly recommended. There are reports on the effectiveness of combination chemotherapy in colon cancer and it has been practiced in clinics for long time. These approaches are associated with toxic side effects. Later, the drug delivery research had shown the potential of nanoencapsulation techniques and active targeting as an effective method to improve the effectiveness of chemotherapy with less toxicity. This current focus article provides a brief analysis of the ongoing research in the colon cancer area using the combinatorial nanomedicines and its outcome. © 2015 Wiley Periodicals, Inc.
Characterizing the combinatorial beam angle selection problem
International Nuclear Information System (INIS)
Bangert, Mark; Ziegenhein, Peter; Oelfke, Uwe
2012-01-01
The beam angle selection (BAS) problem in intensity-modulated radiation therapy is often interpreted as a combinatorial optimization problem, i.e. finding the best combination of η beams in a discrete set of candidate beams. It is well established that the combinatorial BAS problem may be solved efficiently with metaheuristics such as simulated annealing or genetic algorithms. However, the underlying parameters of the optimization process, such as the inclusion of non-coplanar candidate beams, the angular resolution in the space of candidate beams, and the number of evaluated beam ensembles as well as the relative performance of different metaheuristics have not yet been systematically investigated. We study these open questions in a meta-analysis of four strategies for combinatorial optimization in order to provide a reference for future research related to the BAS problem in intensity-modulated radiation therapy treatment planning. We introduce a high-performance inverse planning engine for BAS. It performs a full fluence optimization for ≈3600 treatment plans per hour while handling up to 50 GB of dose influence data (≈1400 candidate beams). For three head and neck patients, we compare the relative performance of a genetic, a cross-entropy, a simulated annealing and a naive iterative algorithm. The selection of ensembles with 5, 7, 9 and 11 beams considering either only coplanar or all feasible candidate beams is studied for an angular resolution of 5°, 10°, 15° and 20° in the space of candidate beams. The impact of different convergence criteria is investigated in comparison to a fixed termination after the evaluation of 10 000 beam ensembles. In total, our simulations comprise a full fluence optimization for about 3000 000 treatment plans. All four combinatorial BAS strategies yield significant improvements of the objective function value and of the corresponding dose distributions compared to standard beam configurations with equi
Combinatorial nuclear level-density model
International Nuclear Information System (INIS)
Uhrenholt, H.; Åberg, S.; Dobrowolski, A.; Døssing, Th.; Ichikawa, T.; Möller, P.
2013-01-01
A microscopic nuclear level-density model is presented. The model is a completely combinatorial (micro-canonical) model based on the folded-Yukawa single-particle potential and includes explicit treatment of pairing, rotational and vibrational states. The microscopic character of all states enables extraction of level-distribution functions with respect to pairing gaps, parity and angular momentum. The results of the model are compared to available experimental data: level spacings at neutron separation energy, data on total level-density functions from the Oslo method, cumulative level densities from low-lying discrete states, and data on parity ratios. Spherical and deformed nuclei follow basically different coupling schemes, and we focus on deformed nuclei
On the Cut-off Point for Combinatorial Group Testing
DEFF Research Database (Denmark)
Fischer, Paul; Klasner, N.; Wegener, I.
1999-01-01
is answered by 1 if Q contains at least one essential object and by 0 otherwise. In the statistical setting the objects are essential, independently of each other, with a given probability p combinatorial setting the number k ... group testing is equal to p* = 12(3 - 5), i.e., the strategy of testing each object individually minimizes the average number of queries iff p >= p* or n = 1. In the combinatorial setting the worst case number of queries is of interest. It has been conjectured that the cut-off point of combinatorial...
Maximization of Tsallis entropy in the combinatorial formulation
International Nuclear Information System (INIS)
Suyari, Hiroki
2010-01-01
This paper presents the mathematical reformulation for maximization of Tsallis entropy S q in the combinatorial sense. More concretely, we generalize the original derivation of Maxwell-Boltzmann distribution law to Tsallis statistics by means of the corresponding generalized multinomial coefficient. Our results reveal that maximization of S 2-q under the usual expectation or S q under q-average using the escort expectation are naturally derived from the combinatorial formulations for Tsallis statistics with respective combinatorial dualities, that is, one for additive duality and the other for multiplicative duality.
Ye, Yusen; Gao, Lin; Zhang, Shihua
2017-01-01
Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions. PMID:29033978
Azimi, Sayyed M; Sheridan, Steven D; Ghannad-Rezaie, Mostafa; Eimon, Peter M; Yanik, Mehmet Fatih
2018-05-01
Identification of optimal transcription-factor expression patterns to direct cellular differentiation along a desired pathway presents significant challenges. We demonstrate massively combinatorial screening of temporally-varying mRNA transcription factors to direct differentiation of neural progenitor cells using a dynamically-reconfigurable magnetically-guided spotting technology for localizing mRNA, enabling experiments on millimetre size spots. In addition, we present a time-interleaved delivery method that dramatically reduces fluctuations in the delivered transcription-factor copy-numbers per cell. We screened combinatorial and temporal delivery of a pool of midbrain-specific transcription factors to augment the generation of dopaminergic neurons. We show that the combinatorial delivery of LMX1A, FOXA2 and PITX3 is highly effective in generating dopaminergic neurons from midbrain progenitors. We show that LMX1A significantly increases TH -expression levels when delivered to neural progenitor cells either during proliferation or after induction of neural differentiation, while FOXA2 and PITX3 increase expression only when delivered prior to induction, demonstrating temporal dependence of factor addition. © 2018, Azimi et al.
International Nuclear Information System (INIS)
Kim, Bong Gon; Kim, Jae Sang; Kim, Jin Eun; Lee, Boo Yeon
2006-06-01
This book introduces complex chemistry with ten chapters, which include development of complex chemistry on history coordination theory and Warner's coordination theory and new development of complex chemistry, nomenclature on complex with conception and define, chemical formula on coordination compound, symbol of stereochemistry, stereo structure and isomerism, electron structure and bond theory on complex, structure of complex like NMR and XAFS, balance and reaction on solution, an organo-metallic chemistry, biology inorganic chemistry, material chemistry of complex, design of complex and calculation chemistry.
Trinajstić, Nenad; Gutman, Ivan
2002-01-01
A brief description is given of the historical development of mathematics and chemistry. A path leading to the meeting of these two sciences is described. An attempt is made to define mathematical chemistry, and journals containing the term mathematical chemistry in their titles are noted. In conclusion, the statement is made that although chemistry is an experimental science aimed at preparing new compounds and materials, mathematics is very useful in chemistry, among other things, to produc...
Hati, Sanchita; Bhattacharyya, Sudeep
2016-01-01
A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…
International Nuclear Information System (INIS)
Kuppermann, A.
1975-01-01
Research progress in the following areas is reported: low energy electron scattering; photoelectron spectrometry; elementary reactions by photolysis at variable wavelengths; collisions in crossed molecular beams; and, diffusion kinetics in the radiation chemistry of water. Publications related to the work are included. (JGB)
Hansen, T. A. R.; Colsters, P. G. J.; M. C. M. van de Sanden,; Engeln, R.
2011-01-01
The gas flow in a linear plasma reactor and the plasma chemistry during hydrogenated amorphous carbon and graphite etching are investigated via time and spatially resolved measurements of the ion density and CH emission. A convolution of the ion and hydrocarbon density shows the importance of charge
Czech Academy of Sciences Publication Activity Database
Habartová, Alena; Valsaraj, K. T.; Roeselová, Martina
2013-01-01
Roč. 117, č. 38 (2013), s. 9205-9215 ISSN 1089-5639 R&D Projects: GA ČR GA13-06181S Institutional support: RVO:61388963 Keywords : aerosol * air bubbles * interfacial concentration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.775, year: 2013
International Nuclear Information System (INIS)
Kilpin, P.; Hupa, M.; Glarborg, P.
1992-01-01
No reduction chemistry in natural gas (methane) reburning was studied using detailed kinetic modeling. A reaction set including 225 reversible elementary gas-phase reactions and 48 chemical species was applied to an ideal plug flow reactor, and the most important reactions leading to NO reduction were identified and quantified for a number of conditions relevant for natural gas reburning. In addition, the influence of different process parameters on the NO reduction was investigated in the reburn zone and burn-out zone, respectively. Further, comparison of the calculations to available laboratory-scale data on reburning is made. In this paper, the impact of various fluid dynamic, mixing, and chemical effects---not accounted for in the calculations---on the NO reduction and the optimum reburning conditions predicted is discussed
Geometric differential evolution for combinatorial and programs spaces.
Moraglio, A; Togelius, J; Silva, S
2013-01-01
Geometric differential evolution (GDE) is a recently introduced formal generalization of traditional differential evolution (DE) that can be used to derive specific differential evolution algorithms for both continuous and combinatorial spaces retaining the same geometric interpretation of the dynamics of the DE search across representations. In this article, we first review the theory behind the GDE algorithm, then, we use this framework to formally derive specific GDE for search spaces associated with binary strings, permutations, vectors of permutations and genetic programs. The resulting algorithms are representation-specific differential evolution algorithms searching the target spaces by acting directly on their underlying representations. We present experimental results for each of the new algorithms on a number of well-known problems comprising NK-landscapes, TSP, and Sudoku, for binary strings, permutations, and vectors of permutations. We also present results for the regression, artificial ant, parity, and multiplexer problems within the genetic programming domain. Experiments show that overall the new DE algorithms are competitive with well-tuned standard search algorithms.
A Combinatorial Kin Discrimination System in Bacillus subtilis.
Lyons, Nicholas A; Kraigher, Barbara; Stefanic, Polonca; Mandic-Mulec, Ines; Kolter, Roberto
2016-03-21
Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell-surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles. Copyright © 2016 Elsevier Ltd. All rights reserved.
Implementation of a combinatorial cleavage and deprotection scheme
DEFF Research Database (Denmark)
Nielsen, John; Rasmussen, Palle H.
1996-01-01
Phthalhydrazide libraries are synthesized in solution from substituted hydrazines and phthalimides in several different library formats including single compounds, indexed sub-libraries and a full library. When carried out during solid-phase synthesis, this combinatorial cleavage and deprotection...
ON 3-WAY COMBINATORIAL IDENTITIES A. K. AGARWAL MEGHA ...
Indian Academy of Sciences (India)
36
∗Corresponding author: Department of Basic and Applied Sciences, University College of Engineering,. Punjabi ... In this paper we provide combinatorial meanings to two generalized basic ... 2010 Mathematics Subject Classification. 05A15 ...
Analysis and design of algorithms for combinatorial problems
Ausiello, G
1985-01-01
Combinatorial problems have been from the very beginning part of the history of mathematics. By the Sixties, the main classes of combinatorial problems had been defined. During that decade, a great number of research contributions in graph theory had been produced, which laid the foundations for most of the research in graph optimization in the following years. During the Seventies, a large number of special purpose models were developed. The impressive growth of this field since has been strongly determined by the demand of applications and influenced by the technological increases in computing power and the availability of data and software. The availability of such basic tools has led to the feasibility of the exact or well approximate solution of large scale realistic combinatorial optimization problems and has created a number of new combinatorial problems.
International Nuclear Information System (INIS)
Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu
2014-01-01
In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for
The Combinatorial Rigidity Conjecture is False for Cubic Polynomials
DEFF Research Database (Denmark)
Henriksen, Christian
2003-01-01
We show that there exist two cubic polynomials with connected Julia sets which are combinatorially equivalent but not topologically conjugate on their Julia sets. This disproves a conjecture by McMullen from 1995.......We show that there exist two cubic polynomials with connected Julia sets which are combinatorially equivalent but not topologically conjugate on their Julia sets. This disproves a conjecture by McMullen from 1995....
Distributing the computation in combinatorial optimization experiments over the cloud
Mario Brcic; Nikica Hlupic; Nenad Katanic
2017-01-01
Combinatorial optimization is an area of great importance since many of the real-world problems have discrete parameters which are part of the objective function to be optimized. Development of combinatorial optimization algorithms is guided by the empirical study of the candidate ideas and their performance over a wide range of settings or scenarios to infer general conclusions. Number of scenarios can be overwhelming, especially when modeling uncertainty in some of the problem’s parameters....
Enabling high performance computational science through combinatorial algorithms
International Nuclear Information System (INIS)
Boman, Erik G; Bozdag, Doruk; Catalyurek, Umit V; Devine, Karen D; Gebremedhin, Assefaw H; Hovland, Paul D; Pothen, Alex; Strout, Michelle Mills
2007-01-01
The Combinatorial Scientific Computing and Petascale Simulations (CSCAPES) Institute is developing algorithms and software for combinatorial problems that play an enabling role in scientific and engineering computations. Discrete algorithms will be increasingly critical for achieving high performance for irregular problems on petascale architectures. This paper describes recent contributions by researchers at the CSCAPES Institute in the areas of load balancing, parallel graph coloring, performance improvement, and parallel automatic differentiation
On the combinatorial foundations of Regge-calculus
International Nuclear Information System (INIS)
Budach, L.
1989-01-01
Lipschitz-Killing curvatures of piecewise flat spaces are combinatorial analogues of Lipschitz-Killing curvatures of Riemannian manifolds. In the following paper rigorous combinatorial representations and proofs of all basic results for Lipschitz-Killing curvatures not using analytic arguments are given. The principal tools for an elementary representation of Regge calculus can be developed by means of basic properties of dihedral angles. (author)
Immune-Stimulating Combinatorial Therapy for Prostate Cancer
2016-10-01
Overlap: None 20 90061946 (Drake) Title: Epigenetic Drugs and Immuno Therapy for Prostate Cancer (EDIT-PC) Effort: 1.2 calendar months (10% effort...AWARD NUMBER: W81XWH-15-1-0667 TITLE: Immune-Stimulating Combinatorial Therapy for Prostate Cancer PRINCIPAL INVESTIGATOR: Robert Ivkov...Stimulating Combinatorial Therapy for Prostate Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-15-1-0667 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S
Enabling high performance computational science through combinatorial algorithms
Energy Technology Data Exchange (ETDEWEB)
Boman, Erik G [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Bozdag, Doruk [Biomedical Informatics, and Electrical and Computer Engineering, Ohio State University (United States); Catalyurek, Umit V [Biomedical Informatics, and Electrical and Computer Engineering, Ohio State University (United States); Devine, Karen D [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Gebremedhin, Assefaw H [Computer Science and Center for Computational Science, Old Dominion University (United States); Hovland, Paul D [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Pothen, Alex [Computer Science and Center for Computational Science, Old Dominion University (United States); Strout, Michelle Mills [Computer Science, Colorado State University (United States)
2007-07-15
The Combinatorial Scientific Computing and Petascale Simulations (CSCAPES) Institute is developing algorithms and software for combinatorial problems that play an enabling role in scientific and engineering computations. Discrete algorithms will be increasingly critical for achieving high performance for irregular problems on petascale architectures. This paper describes recent contributions by researchers at the CSCAPES Institute in the areas of load balancing, parallel graph coloring, performance improvement, and parallel automatic differentiation.
Combinatorial Dyson-Schwinger equations and inductive data types
Kock, Joachim
2016-06-01
The goal of this contribution is to explain the analogy between combinatorial Dyson-Schwinger equations and inductive data types to a readership of mathematical physicists. The connection relies on an interpretation of combinatorial Dyson-Schwinger equations as fixpoint equations for polynomial functors (established elsewhere by the author, and summarised here), combined with the now-classical fact that polynomial functors provide semantics for inductive types. The paper is expository, and comprises also a brief introduction to type theory.
Bowers, Michael T
1979-01-01
Gas Phase Ion Chemistry, Volume 1 covers papers on the advances of gas phase ion chemistry. The book discusses the advances in flow tubes and the measurement of ion-molecule rate coefficients and product distributions; the ion chemistry of the earth's atmosphere; and the classical ion-molecule collision theory. The text also describes statistical methods in reaction dynamics; the state selection by photoion-photoelectron coincidence; and the effects of temperature and pressure in the kinetics of ion-molecule reactions. The energy distribution in the unimolecular decomposition of ions, as well
International Nuclear Information System (INIS)
Antonow, Dyeison; Eifler-Lima, Vera Lucia; Mahler, S. Graciela; Serra, Gloria L.; Manta, Eduardo
2005-01-01
Microwave-assisted solid-phase synthesis of the 2,4-disubstituted thiazole 3 on Merrifield Resin is described. The hydroxyl moiety was converted to amine in five steps - including coupling and cleavage - within a total reaction time of 2 hours and 26% overall yield. The entire solid-phase synthesis was efficiently monitored by FT-IR/KBr pellets and allows potential use in combinatorial chemistry. (author)
Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization.
Hartenfeller, Markus; Proschak, Ewgenij; Schüller, Andreas; Schneider, Gisbert
2008-07-01
We present a fast stochastic optimization algorithm for fragment-based molecular de novo design (COLIBREE, Combinatorial Library Breeding). The search strategy is based on a discrete version of particle swarm optimization. Molecules are represented by a scaffold, which remains constant during optimization, and variable linkers and side chains. Different linkers represent virtual chemical reactions. Side-chain building blocks were obtained from pseudo-retrosynthetic dissection of large compound databases. Here, ligand-based design was performed using chemically advanced template search (CATS) topological pharmacophore similarity to reference ligands as fitness function. A weighting scheme was included for particle swarm optimization-based molecular design, which permits the use of many reference ligands and allows for positive and negative design to be performed simultaneously. In a case study, the approach was applied to the de novo design of potential peroxisome proliferator-activated receptor subtype-selective agonists. The results demonstrate the ability of the technique to cope with large combinatorial chemistry spaces and its applicability to focused library design. The technique was able to perform exploitation of a known scheme and at the same time explorative search for novel ligands within the framework of a given molecular core structure. It thereby represents a practical solution for compound screening in the early hit and lead finding phase of a drug discovery project.
Shende, Pravin; Patil, Sampada; Gaud, R S
2017-07-01
The aim of the present study was to use a combinatorial approach of inclusion complexation and dendrimer synthesization of gefitinib using solvent-free technique for targeting EGFR-TK to treat Non-Small-Cell Lung Cancer (NSCLC). The inclusion complex of gefitinib with β-cyclodextrin was prepared by trituration method. This complex encapsulated G4 PAMAM dendrimers were synthesized by Michael addition and amidation reactions using green chemistry and then PEGylated by conjugation reaction. FTIR and DSC confirmed the formation of inclusion complex of gefitinib and β-cyclodextrin and PEGylation of G4 PAMAM dendrimers. Gefitinib showed higher solubility, encapsulation efficiency and controlled release profile from PEGylated dendrimers compared to inclusion complex. The PEGylated dendrimers of inclusion complex of gefitinib were found to reduce hemolytic toxicity and lesser GI 50 value on Human lung cancer cell line A-549 by effective targeting EGFR-TK. A combinatorial approach of inclusion complexation and dendrimer synthesization is one of the alternative advanced approaches to treat NSCLC. Copyright © 2017 Elsevier B.V. All rights reserved.
A combinatorial approach to angiosperm pollen morphology.
Mander, Luke
2016-11-30
Angiosperms (flowering plants) are strikingly diverse. This is clearly expressed in the morphology of their pollen grains, which are characterized by enormous variety in their shape and patterning. In this paper, I approach angiosperm pollen morphology from the perspective of enumerative combinatorics. This involves generating angiosperm pollen morphotypes by algorithmically combining character states and enumerating the results of these combinations. I use this approach to generate 3 643 200 pollen morphotypes, which I visualize using a parallel-coordinates plot. This represents a raw morphospace. To compare real-world and theoretical morphologies, I map the pollen of 1008 species of Neotropical angiosperms growing on Barro Colorado Island (BCI), Panama, onto this raw morphospace. This highlights that, in addition to their well-documented taxonomic diversity, Neotropical rainforests also represent an enormous reservoir of morphological diversity. Angiosperm pollen morphospace at BCI has been filled mostly by pollen morphotypes that are unique to single plant species. Repetition of pollen morphotypes among higher taxa at BCI reflects both constraint and convergence. This combinatorial approach to morphology addresses the complexity that results from large numbers of discrete character combinations and could be employed in any situation where organismal form can be captured by discrete morphological characters. © 2016 The Author(s).
Exact combinatorial approach to finite coagulating systems
Fronczak, Agata; Chmiel, Anna; Fronczak, Piotr
2018-02-01
This paper outlines an exact combinatorial approach to finite coagulating systems. In this approach, cluster sizes and time are discrete and the binary aggregation alone governs the time evolution of the systems. By considering the growth histories of all possible clusters, an exact expression is derived for the probability of a coagulating system with an arbitrary kernel being found in a given cluster configuration when monodisperse initial conditions are applied. Then this probability is used to calculate the time-dependent distribution for the number of clusters of a given size, the average number of such clusters, and that average's standard deviation. The correctness of our general expressions is proved based on the (analytical and numerical) results obtained for systems with the constant kernel. In addition, the results obtained are compared with the results arising from the solutions to the mean-field Smoluchowski coagulation equation, indicating its weak points. The paper closes with a brief discussion on the extensibility to other systems of the approach presented herein, emphasizing the issue of arbitrary initial conditions.
Scalable Combinatorial Tools for Health Disparities Research
Directory of Open Access Journals (Sweden)
Michael A. Langston
2014-10-01
Full Text Available Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size and heterogeneity of available data needed to illuminate latent gene x environment interactions. This has prompted the adaptation and application of scalable combinatorial methods, many from genome science research, to the study of population health. Most of these powerful tools are algorithmically sophisticated, highly automated and mathematically abstract. Their utility motivates the main theme of this paper, which is to describe real applications of innovative transdisciplinary models and analyses in an effort to help move the research community closer toward identifying the causal mechanisms and associated environmental contexts underlying health disparities. The public health exposome is used as a contemporary focus for addressing the complex nature of this subject.
Combinatorial effects of odorants on mouse behavior
Saraiva, Luis R.; Kondoh, Kunio; Ye, Xiaolan; Yoon, Kyoung-hye; Hernandez, Marcus; Buck, Linda B.
2016-01-01
The mechanisms by which odors induce instinctive behaviors are largely unknown. Odor detection in the mouse nose is mediated by >1, 000 different odorant receptors (ORs) and trace amine-associated receptors (TAARs). Odor perceptions are encoded combinatorially by ORs and can be altered by slight changes in the combination of activated receptors. However, the stereotyped nature of instinctive odor responses suggests the involvement of specific receptors and genetically programmed neural circuits relatively immune to extraneous odor stimuli and receptor inputs. Here, we report that, contrary to expectation, innate odor-induced behaviors can be context-dependent. First, different ligands for a given TAAR can vary in behavioral effect. Second, when combined, some attractive and aversive odorants neutralize one another’s behavioral effects. Both a TAAR ligand and a common odorant block aversion to a predator odor, indicating that this ability is not unique to TAARs and can extend to an aversive response of potential importance to survival. In vitro testing of single receptors with binary odorant mixtures indicates that behavioral blocking can occur without receptor antagonism in the nose. Moreover, genetic ablation of a single receptor prevents its cognate ligand from blocking predator odor aversion, indicating that the blocking requires sensory input from the receptor. Together, these findings indicate that innate odor-induced behaviors can depend on context, that signals from a single receptor can block innate odor aversion, and that instinctive behavioral responses to odors can be modulated by interactions in the brain among signals derived from different receptors. PMID:27208093
School Science Review, 1976
1976-01-01
Described are eight chemistry experiments and demonstrations applicable to introductory chemistry courses. Activities include: measure of lattice enthalpy, Le Chatelier's principle, decarboxylation of soap, use of pocket calculators in pH measurement, and making nylon. (SL)
The Chemistry Dashboard is part of a suite of dashboards developed by EPA to help evaluate the safety of chemicals. The Chemistry Dashboard provides access to a variety of information on over 700,000 chemicals currently in use.
Green, James
1964-01-01
Positronium Chemistry focuses on the methodologies, reactions, processes, and transformations involved in positronium chemistry. The publication first offers information on positrons and positronium and experimental methods, including mesonic atoms, angular correlation measurements, annihilation spectra, and statistical errors in delayed coincidence measurements. The text then ponders on positrons in gases and solids. The manuscript takes a look at the theoretical chemistry of positronium and positronium chemistry in gases. Topics include quenching, annihilation spectrum, delayed coincidence
Lessel, Uta; Wellenzohn, Bernd; Fischer, J Robert; Rarey, Matthias
2012-02-27
A case study is presented illustrating the design of a focused CDK2 library. The scaffold of the library was detected by a feature trees search in a fragment space based on reactions from combinatorial chemistry. For the design the software LoFT (Library optimizer using Feature Trees) was used. The special feature called FTMatch was applied to restrict the parts of the queries where the reagents are permitted to match. This way a 3D scoring function could be simulated. Results were compared with alternative designs by GOLD docking and ROCS 3D alignments.
Bell, Suzanne
2009-07-01
Forensic chemistry is unique among chemical sciences in that its research, practice, and presentation must meet the needs of both the scientific and the legal communities. As such, forensic chemistry research is applied and derivative by nature and design, and it emphasizes metrology (the science of measurement) and validation. Forensic chemistry has moved away from its analytical roots and is incorporating a broader spectrum of chemical sciences. Existing forensic practices are being revisited as the purview of forensic chemistry extends outward from drug analysis and toxicology into such diverse areas as combustion chemistry, materials science, and pattern evidence.
Andersen, A.; Govind, N.; Laskin, A.
2017-12-01
Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.
Physical interpretation of the combinatorial hierarchy
International Nuclear Information System (INIS)
Bastin, T.; Noyes, H.P.
1978-01-01
The combinatorial hierarchy model for base particle processes is compared and contrasted with the Ur-theory as developed at the Tutzing Conferences. It agrees with Ur-theory about a finite basis, the ''fixed past--uncertain future'' aspects of physics, and the necessity of dropping Bohr's requirement of reduction to the haptic language of commonsense and classical physics. However, it retains a constructive, hierarchial approach with can yield only an approximate and discrete ''space time'', and introduces the observation metaphysic at the start. Concrete interpretation of the four levels of the hierarchy (with cardinals 3, 7, 127, 2 127 -1 approx. =10 38 ) associates the three levels which map up and down with three absolute conservation laws (charge, baryon number, lepton number) and the spin dichotomy. The first level represents +, -, and +- unit charge. The second has the quantum nubmers of a baryon--antibaryon pair and associated charged meson (e.g., n anti n, p anti n, p anti p, n anti p, π + , π 0 , π - ). The third level associates this pair, now including four spin states as well as four charge states, with a neutral lepton--antilepton pair (e anti e or ν anti ν) in four spin states (total, 64 states): three charged spinless, three charged spin-1, and neutral spin-1 mesons (15 states), and a neutral vector boson associated with the leptons; this gives 3 + 15 + 3 x 15 = 63 possible boson states, so a total correct count of 63 + 64 = 127 states. Something like SU 2 X SU 3 and other indications of quark quantum numbers can occur as substructures at the fourth (unstable) level. A slight extension gives the usual static approximation to the building energy of the hydrogen atom, α 2 m/sub e/c 2 . Cosmological implications of the theory are in accord with current experience. A beginning in the physical interpretation of a theory which could eventually encompass all branches of physics was made. 3 figures, 6 tables
Klagkou, Katerina; Pullen, Frank; Harrison, Mark; Organ, Andy; Firth, Alistair; Langley, G John
2003-01-01
Combinatorial chemistry is widely used within the pharmaceutical industry as a means of rapid identification of potential drugs. With the growth of combinatorial libraries, mass spectrometry (MS) became the key analytical technique because of its speed of analysis, sensitivity, accuracy and ability to be coupled with other analytical techniques. In the majority of cases, electrospray mass spectrometry (ES-MS) has become the default ionisation technique. However, due to the absence of fragment ions in the resulting spectra, tandem mass spectrometry (MS/MS) is required to provide structural information for the identification of an unknown analyte. This work discusses the first steps of an investigation into the fragmentation pathways taking place in electrospray tandem mass spectrometry. The ultimate goal for this project is to set general fragmentation rules for non-peptidic, pharmaceutical, combinatorial compounds. As an aid, an artificial intelligence (AI) software package is used to facilitate interpretation of the spectra. This initial study has focused on determining the fragmentation rules for some classes of compound types that fit the remit as outlined above. Based on studies carried out on several combinatorial libraries of these compounds, it was established that different classes of drug molecules follow unique fragmentation pathways. In addition to these general observations, the specific ionisation processes and the fragmentation pathways involved in the electrospray mass spectra of these systems were explored. The ultimate goal will be to incorporate our findings into the computer program and allow identification of an unknown, non-peptidic compound following insertion of its ES-MS/MS spectrum into the AI package. The work herein demonstrates the potential benefit of such an approach in addressing the issue of high-throughput, automated MS/MS data interpretation. Copyright 2003 John Wiley & Sons, Ltd.
Grant, William B.; Butler, Carolyn F.; Fenn, Marta A.; Kooi, Susan A.; Browell, Edward V.; Fuelberg, Henry
1998-01-01
The NASA Langley Research Center's airborne UV Differential Absorption Lidar (DIAL) system participated in the Subsonic Assessment, Ozone and Nitrogen Oxide Experiment (SONEX) mission from October 13 to November 12, 1997. The purpose of the mission was to study the upper troposphere/lower stratosphere in and near the North Atlantic flight corridor to better understand this region of the atmosphere and how civilian air travel in the corridor might be affecting the atmospheric chemistry. Bases of operations included NASA Ames, California (37.4 deg N, 122.1 deg W); Bangor, Maine (44.8 deg N, 68.8 deg W); Shannon, Ireland (52.7 deg N, 8.9 deg W); and Lajes, Terceira Island, Azores (38.8 deg N, 27.1 deg W). Since the UV DIAL system observes in the nadir as well as the zenith, aerosol and ozone data were obtained from near the Earth's surface to the lower stratosphere. A number of interesting features were noted relating to both chemistry and dynamics of the troposphere, which are reported here.
Morphological Constraints on Cerebellar Granule Cell Combinatorial Diversity.
Gilmer, Jesse I; Person, Abigail L
2017-12-13
Combinatorial expansion by the cerebellar granule cell layer (GCL) is fundamental to theories of cerebellar contributions to motor control and learning. Granule cells (GrCs) sample approximately four mossy fiber inputs and are thought to form a combinatorial code useful for pattern separation and learning. We constructed a spatially realistic model of the cerebellar GCL and examined how GCL architecture contributes to GrC combinatorial diversity. We found that GrC combinatorial diversity saturates quickly as mossy fiber input diversity increases, and that this saturation is in part a consequence of short dendrites, which limit access to diverse inputs and favor dense sampling of local inputs. This local sampling also produced GrCs that were combinatorially redundant, even when input diversity was extremely high. In addition, we found that mossy fiber clustering, which is a common anatomical pattern, also led to increased redundancy of GrC input combinations. We related this redundancy to hypothesized roles of temporal expansion of GrC information encoding in service of learned timing, and we show that GCL architecture produces GrC populations that support both temporal and combinatorial expansion. Finally, we used novel anatomical measurements from mice of either sex to inform modeling of sparse and filopodia-bearing mossy fibers, finding that these circuit features uniquely contribute to enhancing GrC diversification and redundancy. Our results complement information theoretic studies of granule layer structure and provide insight into the contributions of granule layer anatomical features to afferent mixing. SIGNIFICANCE STATEMENT Cerebellar granule cells are among the simplest neurons, with tiny somata and, on average, just four dendrites. These characteristics, along with their dense organization, inspired influential theoretical work on the granule cell layer as a combinatorial expander, where each granule cell represents a unique combination of inputs
The priming of basic combinatory responses in MEG.
Blanco-Elorrieta, Esti; Ferreira, Victor S; Del Prato, Paul; Pylkkänen, Liina
2018-01-01
Priming has been a powerful tool for the study of human memory and especially the memory representations relevant for language. However, although it is well established that lexical access can be primed, we do not know exactly what types of computations can be primed above the word level. This work took a neurobiological approach and assessed the ways in which the complex representation of a minimal combinatory phrase, such as red boat, can be primed, as evidenced by the spatiotemporal profiles of magnetoencephalography (MEG) signals. Specifically, we built upon recent progress on the neural signatures of phrasal composition and tested whether the brain activities implicated for the basic combination of two words could be primed. In two experiments, MEG was recorded during a picture naming task where the prime trials were designed to replicate previously reported combinatory effects and the target trials to test whether those combinatory effects could be primed. The manipulation of the primes was successful in eliciting larger activity for adjective-noun combinations than single nouns in left anterior temporal and ventromedial prefrontal cortices, replicating prior MEG studies on parallel contrasts. Priming of similarly timed activity was observed during target trials in anterior temporal cortex, but only when the prime and target shared an adjective. No priming in temporal cortex was observed for single word repetition and two control tasks showed that the priming effect was not elicited if the prime pictures were simply viewed but not named. In sum, this work provides evidence that very basic combinatory operations can be primed, with the necessity for some lexical overlap between prime and target suggesting combinatory conceptual, as opposed to syntactic processing. Both our combinatory and priming effects were early, onsetting between 100 and 150ms after picture onset and thus are likely to reflect the very earliest planning stages of a combinatory message
Müller, Achim; Gouzerh, Pierre
2012-11-21
Following Nature's lessons, today chemists can cross the boundary of the small molecule world to construct multifunctional and highly complex molecular nano-objects up to protein size and even cell-like nanosystems showing responsive sensing. Impressive examples emerge from studies of the solutions of some oxoanions of the early transition metals especially under reducing conditions which enable the controlled linking of metal-oxide building blocks. The latter are available from constitutional dynamic libraries, thus providing the option to generate multifunctional unique nanoscale molecular systems with exquisite architectures, which even opens the way towards adaptive and evolutive (Darwinian) chemistry. The present review presents the first comprehensive report of current knowledge (including synthesis aspects not discussed before) regarding the related giant metal-oxide clusters mainly of the type {Mo(57)M'(6)} (M' = Fe(III), V(IV)) (torus structure), {M(72)M'(30)} (M = Mo, M' = V(IV), Cr(III), Fe(III), Mo(V)), {M(72)Mo(60)} (M = Mo, W) (Keplerates), {Mo(154)}, {Mo(176)}, {Mo(248)} ("big wheels"), and {Mo(368)} ("blue lemon") - all having the important transferable pentagonal {(M)M(5)} groups in common. These discoveries expanded the frontiers of inorganic chemistry to the mesoscopic world, while there is probably no collection of discrete inorganic compounds which offers such a versatile chemistry and the option to study new phenomena of interdisciplinary interest. The variety of different properties of the sphere- and wheel-type metal-oxide-based clusters can directly be related to their unique architectures: The spherical Keplerate-type capsules having 20 crown-ether-type pores and tunable internal functionalities allow the investigation of confined matter as well as that of sphere-surface-supramolecular and encapsulation chemistry - including related new aspects of the biologically important hydrophobic effects - but also of nanoscale ion transport and
Summation on the basis of combinatorial representation of equal powers
Directory of Open Access Journals (Sweden)
Alexander I. Nikonov
2016-03-01
Full Text Available In the paper the conclusion of combinatorial expressions for the sums of members of several sequences is considered. Conclusion is made on the basis of combinatorial representation of the sum of the weighted equal powers. The weighted members of a geometrical progression, the simple arithmetic-geometrical and combined progressions are subject to summation. One of principal places in the given conclusion occupies representation of members of each of the specified progressions in the form of matrix elements. The row of this matrix is formed with use of a gang of equal powers with the set weight factor. Besides, in work formulas of combinatorial identities with participation of free components of the sums of equal powers, and also separate power-member of sequence of equal powers or a geometrical progression are presented. All presented formulas have the general basis-components of the sums of equal powers.
Combinatorial vector fields and the valley structure of fitness landscapes.
Stadler, Bärbel M R; Stadler, Peter F
2010-12-01
Adaptive (downhill) walks are a computationally convenient way of analyzing the geometric structure of fitness landscapes. Their inherently stochastic nature has limited their mathematical analysis, however. Here we develop a framework that interprets adaptive walks as deterministic trajectories in combinatorial vector fields and in return associate these combinatorial vector fields with weights that measure their steepness across the landscape. We show that the combinatorial vector fields and their weights have a product structure that is governed by the neutrality of the landscape. This product structure makes practical computations feasible. The framework presented here also provides an alternative, and mathematically more convenient, way of defining notions of valleys, saddle points, and barriers in landscape. As an application, we propose a refined approximation for transition rates between macrostates that are associated with the valleys of the landscape.
Recent advances in combinatorial biosynthesis for drug discovery
Directory of Open Access Journals (Sweden)
Sun H
2015-02-01
Full Text Available Huihua Sun,1,* Zihe Liu,1,* Huimin Zhao,1,2 Ee Lui Ang1 1Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore; 2Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA *These authors contributed equally to this work Abstract: Because of extraordinary structural diversity and broad biological activities, natural products have played a significant role in drug discovery. These therapeutically important secondary metabolites are assembled and modified by dedicated biosynthetic pathways in their host living organisms. Traditionally, chemists have attempted to synthesize natural product analogs that are important sources of new drugs. However, the extraordinary structural complexity of natural products sometimes makes it challenging for traditional chemical synthesis, which usually involves multiple steps, harsh conditions, toxic organic solvents, and byproduct wastes. In contrast, combinatorial biosynthesis exploits substrate promiscuity and employs engineered enzymes and pathways to produce novel “unnatural” natural products, substantially expanding the structural diversity of natural products with potential pharmaceutical value. Thus, combinatorial biosynthesis provides an environmentally friendly way to produce natural product analogs. Efficient expression of the combinatorial biosynthetic pathway in genetically tractable heterologous hosts can increase the titer of the compound, eventually resulting in less expensive drugs. In this review, we will discuss three major strategies for combinatorial biosynthesis: 1 precursor-directed biosynthesis; 2 enzyme-level modification, which includes swapping of the entire domains, modules and subunits, site-specific mutagenesis, and directed evolution; 3 pathway-level recombination. Recent examples of combinatorial biosynthesis employing these
International Nuclear Information System (INIS)
2003-08-01
This book with sixteen chapter explains organic chemistry on linkage isomerism such as alkane, cycloalkane, alkene, aromatic compounds, stereo selective isomerization, aromatic compounds, stereo selective isomerization, organic compounds, stereo selective isomerization, organic halogen compound, alcohol, ether, aldehyde and ketone, carboxylic acid, dicarboxylic acid, fat and detergent, amino, carbohydrate, amino acid and protein, nucleotide and nucleic acid and spectroscopy, a polymer and medical chemistry. Each chapter has introduction structure and characteristic and using of organic chemistry.
Energy Technology Data Exchange (ETDEWEB)
None
1973-07-01
Research progress is reported on radiation chemistry of heavy elements that includes the following topics: radiation chemistry of plutonium in nitric acid solutions (spectrophotometric analysis and gamma radiolysis of Pu(IV) and Pu(VI) in nitric acid solution); EPR studies of intermediates formed in radiolytic reactions with aqueous medium; two-phase radiolysis and its effect on the distribution coefficient of plutonium; and radiation chemistry of nitric acid. (DHM)
New electronics stuff chemistry
International Nuclear Information System (INIS)
Byeon, Su Il
2003-04-01
The first part of this book is about equilibrium electrochemistry on electric thermo dynamic equilibrium state of electrochemistry, crystal defect of solid, thermodynamics on defect electron and election in semiconductor, Gawani potential, volta potential and equilibrium potential and thermodynamics application in Gawani battery. The second part deals with dynamic electrochemistry electrode reaction kinetics and corrosion potential in normal state, diffusion and transport of ion and electron and current impedance spectroscopy. It also mentions industrial electrochemistry and laboratory works in electronics chemistry course.
International Nuclear Information System (INIS)
Burns, C.; Bryan, J.; Cotton, F.; Ott, K.; Kubas, G.; Haefner, S.; Barrera, J.; Hall, K.; Burrell, A.
1996-01-01
Technetium chemistry is a young and developing field. Despite the limited knowledge of its chemistry, technetium is the workhorse for nuclear medicine. Technetium is also a significant environmental concern because it is formed as a byproduct of nuclear weapons production and fission-power generators. Development of new technetium radio-pharmaceuticals and effective environmental control depends strongly upon knowledge of basic technetium chemistry. The authors performed research into the basic coordination and organometallic chemistry of technetium and used this knowledge to address nuclear medicine and environmental applications. This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL)
Federal Laboratory Consortium — Chemistry technology experts at NCATS engage in a variety of innovative translational research activities, including:Design of bioactive small molecules.Development...
Thalos, Mariam
2013-01-01
Chemistry possesses a distinctive theoretical lens--a distinctive set of theoretical concerns regarding the dynamics and transformations of a perplexing variety of organic and nonorganic substances--to which it must be faithful. Even if it is true that chemical facts bear a special (reductive) relationship to physical facts, nonetheless it will…
Combinatorial methods for advanced materials research and development
Energy Technology Data Exchange (ETDEWEB)
Cremer, R.; Dondorf, S.; Hauck, M.; Horbach, D.; Kaiser, M.; Krysta, S.; Kyrylov, O.; Muenstermann, E.; Philipps, M.; Reichert, K.; Strauch, G. [Rheinisch-Westfaelische Technische Hochschule Aachen (Germany). Lehrstuhl fuer Theoretische Huettenkunde
2001-10-01
The applicability of combinatorial methods in developing advanced materials is illustrated presenting four examples for the deposition and characterization of one- and two-dimensionally laterally graded coatings, which were deposited by means of (reactive) magnetron sputtering and plasma-enhanced chemical vapor deposition. To emphasize the advantages of combinatorial approaches, metastable hard coatings like (Ti,Al)N and (Ti,Al,Hf)N respectively, as well as Ge-Sb-Te based films for rewritable optical data storage were investigated with respect to the relations between structure, composition, and the desired materials properties. (orig.)
Combinatorial algebraic geometry selected papers from the 2016 apprenticeship program
Sturmfels, Bernd
2017-01-01
This volume consolidates selected articles from the 2016 Apprenticeship Program at the Fields Institute, part of the larger program on Combinatorial Algebraic Geometry that ran from July through December of 2016. Written primarily by junior mathematicians, the articles cover a range of topics in combinatorial algebraic geometry including curves, surfaces, Grassmannians, convexity, abelian varieties, and moduli spaces. This book bridges the gap between graduate courses and cutting-edge research by connecting historical sources, computation, explicit examples, and new results.
Combinatorial reasoning an introduction to the art of counting
DeTemple, Duane
2014-01-01
Written by well-known scholars in the field, this book introduces combinatorics alongside modern techniques, showcases the interdisciplinary aspects of the topic, and illustrates how to problem solve with a multitude of exercises throughout. The authors' approach is very reader-friendly and avoids the ""scholarly tone"" found in many books on this topic. Combinatorial Reasoning: An Introduction to the Art of Counting: Focuses on enumeration and combinatorial thinking as a way to develop a variety of effective approaches to solving counting problemsIncludes brief summaries of basic concepts f
Mitigation of Control Channel Jamming via Combinatorial Key Distribution
Falahati, Abolfazl; Azarafrooz, Mahdi
The problem of countering control channel jamming against internal adversaries in wireless ad hoc networks is addressed. Using combinatorial key distribution, a new method to secure the control channel access is introduced. This method, utilizes the established keys in the key establishment phase to hide the location of control channels without the need for a secure BS. This is in obtained by combination of a collision free one-way function and a combinatorial key establishment method. The proposed scheme can be considered as a special case of the ALOHA random access schemes which uses the common established keys as its seeds to generate the pattern of transmission.
Polyhedral and semidefinite programming methods in combinatorial optimization
Tunçel, Levent
2010-01-01
Since the early 1960s, polyhedral methods have played a central role in both the theory and practice of combinatorial optimization. Since the early 1990s, a new technique, semidefinite programming, has been increasingly applied to some combinatorial optimization problems. The semidefinite programming problem is the problem of optimizing a linear function of matrix variables, subject to finitely many linear inequalities and the positive semidefiniteness condition on some of the matrix variables. On certain problems, such as maximum cut, maximum satisfiability, maximum stable set and geometric r
Some results from the combinatorial approach to quantum logic
International Nuclear Information System (INIS)
Greechie, R.J.
1976-01-01
The combinatorial approach to quantum logic focuses on certain interconnections between graphs, combinatorial designs, and convex sets as applied to a quantum logic. This article is concerned only with orthomodular lattices and associated structures. A class of complete atomic irreducible semimodular orthomodular lattices is derived which may not be represented as linear subspaces of a vector space over a division ring. Each of these lattices is a proposition system of dimension three. These proposition systems form orthocomplemented non-Desarguesian projective geometries. (B.R.H.)
Markov's theorem and algorithmically non-recognizable combinatorial manifolds
International Nuclear Information System (INIS)
Shtan'ko, M A
2004-01-01
We prove the theorem of Markov on the existence of an algorithmically non-recognizable combinatorial n-dimensional manifold for every n≥4. We construct for the first time a concrete manifold which is algorithmically non-recognizable. A strengthened form of Markov's theorem is proved using the combinatorial methods of regular neighbourhoods and handle theory. The proofs coincide for all n≥4. We use Borisov's group with insoluble word problem. It has two generators and twelve relations. The use of this group forms the base for proving the strengthened form of Markov's theorem
On some interconnections between combinatorial optimization and extremal graph theory
Directory of Open Access Journals (Sweden)
Cvetković Dragoš M.
2004-01-01
Full Text Available The uniting feature of combinatorial optimization and extremal graph theory is that in both areas one should find extrema of a function defined in most cases on a finite set. While in combinatorial optimization the point is in developing efficient algorithms and heuristics for solving specified types of problems, the extremal graph theory deals with finding bounds for various graph invariants under some constraints and with constructing extremal graphs. We analyze by examples some interconnections and interactions of the two theories and propose some conclusions.
Energy Technology Data Exchange (ETDEWEB)
Moon, Sung Won [KIST Gangneung Institute, Gangneung (Korea, Republic of); Ham, Jungyeob [Gangneung-Wonju National University, Gangneung (Korea, Republic of); Chang, Young-Tae [National University of Singapore, Singapore (Singapore); Lee, Jae Wook [University of Science and Technology, Daejon (Korea, Republic of)
2015-01-15
In combinatorial chemistry, solid-phase synthesis is a popular approach formass production of small molecules. Compared to solution-phase synthesis, it is easy to prepare and purify a large number of heterocyclic small molecules via solid-phase chemistry; the overall reaction time is decreased as well. 1,3,5-Triazine is a nitrogen-containing heterocyclic aromatic scaffold that was shown to be a druggable scaffold in recent studies. These structures have been reported as anticancer, antimicrobial, and antiretroviral compounds, as CDKs and p38 MAP kinase inhibitors, as estrogen receptor modulators, and as inosine monophosphate dehydrogenase inhibitors. we designed and synthesized disubstituted triazine compounds as an analog of disubstituted pyrimidine compounds. These disubstituted triazine compounds possess a linear structure which may have biological activity similar to that of disubstituted pyrimidine. Here we report the solid-phase synthesis of disubstituted triazine compounds.
International Nuclear Information System (INIS)
Moon, Sung Won; Ham, Jungyeob; Chang, Young-Tae; Lee, Jae Wook
2015-01-01
In combinatorial chemistry, solid-phase synthesis is a popular approach formass production of small molecules. Compared to solution-phase synthesis, it is easy to prepare and purify a large number of heterocyclic small molecules via solid-phase chemistry; the overall reaction time is decreased as well. 1,3,5-Triazine is a nitrogen-containing heterocyclic aromatic scaffold that was shown to be a druggable scaffold in recent studies. These structures have been reported as anticancer, antimicrobial, and antiretroviral compounds, as CDKs and p38 MAP kinase inhibitors, as estrogen receptor modulators, and as inosine monophosphate dehydrogenase inhibitors. we designed and synthesized disubstituted triazine compounds as an analog of disubstituted pyrimidine compounds. These disubstituted triazine compounds possess a linear structure which may have biological activity similar to that of disubstituted pyrimidine. Here we report the solid-phase synthesis of disubstituted triazine compounds
Garcia, R. R.
1986-01-01
The influence of breaking gravity waves on the dynamics and chemical composition of the 60 to 110 km region is investigated with a two dimensional model that includes a parameterization of gravity wave momentum deposition and diffusion. The dynamical model is described by Garcia and Solomon (1983) and Solomon and Garcia (1983) and includes a complete chemical scheme for the mesosphere and lower thermosphere. The parameterization of Lindzen (1981) is used to calculate the momentum deposited and the turbulent diffusion produced by the gravity waves. It is found that wave momentum deposition drives a very vigorous mean meridional circulation, produces a very cold summer mesopause and reverse the zonal wind jets above about 85 km. The seasonal variation of the turbulent diffusion coefficient is consistent with the behavior of mesospheric turbulences inferred from MST radar echoes. The large degree of consistency between model results and various types of dynamical and chemical data supports very strongly the hypothesis that breaking gravity waves play a major role in determining the zonally-averaged dynamical and chemical structure of the 60 to 110 km region of the atmosphere.
Fuson, Michael M.
2017-01-01
Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…
Fast Combinatorial Algorithm for the Solution of Linearly Constrained Least Squares Problems
Van Benthem, Mark H.; Keenan, Michael R.
2008-11-11
A fast combinatorial algorithm can significantly reduce the computational burden when solving general equality and inequality constrained least squares problems with large numbers of observation vectors. The combinatorial algorithm provides a mathematically rigorous solution and operates at great speed by reorganizing the calculations to take advantage of the combinatorial nature of the problems to be solved. The combinatorial algorithm exploits the structure that exists in large-scale problems in order to minimize the number of arithmetic operations required to obtain a solution.
International Nuclear Information System (INIS)
Balestrini, Raffaella; Polesello, Stefano; Sacchi, Elisa
2014-01-01
We monitored the chemical and isotopic compositions of wet depositions, at the Pyramid International Laboratory (5050 m a.s.l.), and surrounding surface waters, in the Khumbu basin, to understand precipitation chemistry and to obtain insights regarding ecosystem responses to atmospheric inputs. The major cations in the precipitation were NH 4 + and Ca 2+ , whereas the main anion was HCO 3 − , which constituted approximately 69% of the anions, followed by NO 3 − , SO 4 2− and Cl − . Data analysis suggested that Na + , Cl − and K + were derived from the long-range transport of marine aerosols. Ca 2+ , Mg 2+ and HCO 3 − were related to rock and soil dust contributions and the NO 3 − and SO 4 2− concentrations were derived from anthropogenic sources. Furthermore, NH 4 + was derived from gaseous NH 3 scavenging. The isotopic composition of weekly precipitation ranged from − 1.9 to − 23.2‰ in δ 18 O, and from − 0.8 to − 174‰ in δ 2 H, with depleted values characterizing the central part of the monsoon period. The chemical composition of the stream water was dominated by calcite and/or gypsum dissolution. However, the isotopic composition of the stream water did not fully reflect the composition of the monsoon precipitation, which suggested that other water sources contributed to the stream flow. Precipitation contents for all ions were the lowest ones among those measured in high elevation sites around the world. During the monsoon periods the depositions were not substantially influenced by anthropogenic inputs, while in pre- and post-monsoon seasons the Himalayas could not represent an effective barrier for airborne pollution. In the late monsoon phase, the increase of ionic contents in precipitation could also be due to a change in the moisture source. The calculated atmospheric N load (0.30 kg ha −1 y −1 ) was considerably lower than the levels that were measured in other high-altitude environments. Nevertheless, the NO 3
Theory of site-specific interactions of the combinatorial transcription factors with DNA
International Nuclear Information System (INIS)
Murugan, R
2010-01-01
We derive a functional relationship between the mean first passage time associated with the concurrent binding of multiple transcription factors (TFs) at their respective combinatorial cis-regulatory module sites (CRMs) and the number n of TFs involved in the regulation of the initiation of transcription of a gene of interest. Our results suggest that the overall search time τ s that is required by the n TFs to locate their CRMs which are all located on the same DNA chain scales with n as τ s ∼n α where α ∼ (2/5). When the jump size k that is associated with the dynamics of all the n TFs along DNA is higher than that of the critical jump size k c that scales with the size of DNA N as k c ∼ N 2/3 , we observe a similar power law scaling relationship and also the exponent α. When k c , α shows a strong dependence on both n and k. Apparently there is a critical number of combinatorial TFs n c ∼ 20 that is required to efficiently regulate the initiation of transcription of a given gene below which (2/5) 1. These results seem to be independent of the initial distances between the TFs and their corresponding CRMs and also suggest that the maximum number of TFs involved in a given combinatorial regulation of the initiation of transcription of a gene of interest seems to be restricted by the degree of condensation of the genomic DNA. The optimum number m opt of roadblock protein molecules per genome at which the search time associated with these n TFs to locate their binding sites is a minimum seems to scale as m opt ∼Ln α/2 where L is the sliding length of TFs whose maximum value seems to be such that L ≤ 10 4 bps for the E. coli bacterial genome.
National Research Council Canada - National Science Library
1997-01-01
Provides in depth reviews on current progress in the fields of asymmetric synthesis, organometallic chemistry, bioorganic chemistry, heterocyclic chemistry, natural product chemistry, and analytical...
International Nuclear Information System (INIS)
Vertes, A.; Kiss, I.
1987-01-01
This book is an introduction to the application of nuclear science in modern chemistry. The first group of chapters discuss the basic phenomena and concepts of nuclear physics with emphasis on their relation to chemical problems, including the main properties and the composition of atomic nuclei, nuclear reactions, radioactive decay and interactions of radiation with matter. These chapters provide the basis for understanding the following chapters which encompass the wide scope of nuclear chemistry. The methods of the investigation of chemical structure based on the interaction of nuclear radiation with matter including positronium chemistry and other exotic atoms is elaborated in particular detail. Separate chapters are devoted to the use of radioactive tracers, the chemical consequences of nuclear processes (i.e. hot atom chemistry), radiation chemistry, isotope effects and their applications, and the operation of nuclear reactors
International Nuclear Information System (INIS)
Vertes, A.; Kiss, I.
1987-01-01
This book is an introduction to the application of nuclear science in modern chemistry. The first group of chapters discuss the basic phenomena and concepts of nuclear physics with emphasis on their relation to chemical problems, including the main properties and the composition of atomic nuclei, nuclear reactions, radioactive decay and interactions of radiation with matter. These chapters provide the basis for understanding the following chapters which encompass the wide scope of nuclear chemistry. The methods of the investigation of chemical structure based on the interaction of nuclear radiation with matter including positronium chemistry and other exotic atoms is elaborated in particular detail. Separate chapters are devoted to the use of radioactive tracers, the chemical consequences of nuclear processes (i.e. hot atom chemistry), radiation chemistry, isotope effects and their applications, and the operation of nuclear reactors. (Auth.)
Energy Technology Data Exchange (ETDEWEB)
Balestrini, Raffaella, E-mail: balestrini@irsa.cnr.it [Water Research Institute, National Research Council (IRSA-CNR), Via del Mulino 19, Brugherio, MB (Italy); Polesello, Stefano [Water Research Institute, National Research Council (IRSA-CNR), Via del Mulino 19, Brugherio, MB (Italy); Sacchi, Elisa [Department of Earth and Environmental Sciences, University of Pavia and IGG-CNR, Via Ferrata 1, 27100 Pavia (Italy)
2014-07-01
We monitored the chemical and isotopic compositions of wet depositions, at the Pyramid International Laboratory (5050 m a.s.l.), and surrounding surface waters, in the Khumbu basin, to understand precipitation chemistry and to obtain insights regarding ecosystem responses to atmospheric inputs. The major cations in the precipitation were NH{sub 4}{sup +} and Ca{sup 2+}, whereas the main anion was HCO{sub 3}{sup −}, which constituted approximately 69% of the anions, followed by NO{sub 3}{sup −}, SO{sub 4}{sup 2−} and Cl{sup −}. Data analysis suggested that Na{sup +}, Cl{sup −} and K{sup +} were derived from the long-range transport of marine aerosols. Ca{sup 2+}, Mg{sup 2+} and HCO{sub 3}{sup −} were related to rock and soil dust contributions and the NO{sub 3}{sup −} and SO{sub 4}{sup 2−} concentrations were derived from anthropogenic sources. Furthermore, NH{sub 4}{sup +} was derived from gaseous NH{sub 3} scavenging. The isotopic composition of weekly precipitation ranged from − 1.9 to − 23.2‰ in δ{sup 18}O, and from − 0.8 to − 174‰ in δ{sup 2}H, with depleted values characterizing the central part of the monsoon period. The chemical composition of the stream water was dominated by calcite and/or gypsum dissolution. However, the isotopic composition of the stream water did not fully reflect the composition of the monsoon precipitation, which suggested that other water sources contributed to the stream flow. Precipitation contents for all ions were the lowest ones among those measured in high elevation sites around the world. During the monsoon periods the depositions were not substantially influenced by anthropogenic inputs, while in pre- and post-monsoon seasons the Himalayas could not represent an effective barrier for airborne pollution. In the late monsoon phase, the increase of ionic contents in precipitation could also be due to a change in the moisture source. The calculated atmospheric N load (0.30 kg ha{sup −1} y{sup −1
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density.
Directory of Open Access Journals (Sweden)
Claudia Coronnello
Full Text Available MicroRNAs (miRNAs are post-transcriptional regulators that bind to their target mRNAs through base complementarity. Predicting miRNA targets is a challenging task and various studies showed that existing algorithms suffer from high number of false predictions and low to moderate overlap in their predictions. Until recently, very few algorithms considered the dynamic nature of the interactions, including the effect of less specific interactions, the miRNA expression level, and the effect of combinatorial miRNA binding. Addressing these issues can result in a more accurate miRNA:mRNA modeling with many applications, including efficient miRNA-related SNP evaluation. We present a novel thermodynamic model based on the Fermi-Dirac equation that incorporates miRNA expression in the prediction of target occupancy and we show that it improves the performance of two popular single miRNA target finders. Modeling combinatorial miRNA targeting is a natural extension of this model. Two other algorithms show improved prediction efficiency when combinatorial binding models were considered. ComiR (Combinatorial miRNA targeting, a novel algorithm we developed, incorporates the improved predictions of the four target finders into a single probabilistic score using ensemble learning. Combining target scores of multiple miRNAs using ComiR improves predictions over the naïve method for target combination. ComiR scoring scheme can be used for identification of SNPs affecting miRNA binding. As proof of principle, ComiR identified rs17737058 as disruptive to the miR-488-5p:NCOA1 interaction, which we confirmed in vitro. We also found rs17737058 to be significantly associated with decreased bone mineral density (BMD in two independent cohorts indicating that the miR-488-5p/NCOA1 regulatory axis is likely critical in maintaining BMD in women. With increasing availability of comprehensive high-throughput datasets from patients ComiR is expected to become an essential
Confluence of an extension of combinatory logic by Boolean constants
DEFF Research Database (Denmark)
Czajka, Łukasz
2017-01-01
We show confluence of a conditional term rewriting system CL-pc1, which is an extension of Combinatory Logic by Boolean constants. This solves problem 15 from the RTA list of open problems. The proof has been fully formalized in the Coq proof assistant....
Combinatorial algorithms enabling computational science: tales from the front
International Nuclear Information System (INIS)
Bhowmick, Sanjukta; Boman, Erik G; Devine, Karen; Gebremedhin, Assefaw; Hendrickson, Bruce; Hovland, Paul; Munson, Todd; Pothen, Alex
2006-01-01
Combinatorial algorithms have long played a crucial enabling role in scientific and engineering computations. The importance of discrete algorithms continues to grow with the demands of new applications and advanced architectures. This paper surveys some recent developments in this rapidly changing and highly interdisciplinary field
Combinatorial structures and processing in neural blackboard architectures
van der Velde, Frank; van der Velde, Frank; de Kamps, Marc; Besold, Tarek R.; d'Avila Garcez, Artur; Marcus, Gary F.; Miikkulainen, Risto
2015-01-01
We discuss and illustrate Neural Blackboard Architectures (NBAs) as the basis for variable binding and combinatorial processing the brain. We focus on the NBA for sentence structure. NBAs are based on the notion that conceptual representations are in situ, hence cannot be copied or transported.
Anti-termite efficacy of Capparis decidua and its combinatorial ...
African Journals Online (AJOL)
Michael Horsfall
ABSTRACT: Capparis deciduas and its combinatorial mixtures were evaluated to observe the anti-termite efficacy against Indian white termite Odontotermes obesus. These have shown very high termiticidal activity and wood protection in the soil. It is proved by very low LD50 values i.e. 0.0218mg/g and 0.021mg/g obtained ...
Combinatorial algorithms enabling computational science: tales from the front
Energy Technology Data Exchange (ETDEWEB)
Bhowmick, Sanjukta [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Boman, Erik G [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Devine, Karen [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Gebremedhin, Assefaw [Computer Science Department, Old Dominion University (United States); Hendrickson, Bruce [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Hovland, Paul [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Munson, Todd [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Pothen, Alex [Computer Science Department, Old Dominion University (United States)
2006-09-15
Combinatorial algorithms have long played a crucial enabling role in scientific and engineering computations. The importance of discrete algorithms continues to grow with the demands of new applications and advanced architectures. This paper surveys some recent developments in this rapidly changing and highly interdisciplinary field.
Some Combinatorial Interpretations and Applications of Fuss-Catalan Numbers
Lin, Chin-Hung
2011-01-01
Fuss-Catalan number is a family of generalized Catalan numbers. We begin by two definitions of Fuss-Catalan numbers and some basic properties. And we give some combinatorial interpretations different from original Catalan numbers. Finally we generalize the Jonah's theorem as its applications.
A Combinatorial Proof of a Result on Generalized Lucas Polynomials
Directory of Open Access Journals (Sweden)
Laugier Alexandre
2016-09-01
Full Text Available We give a combinatorial proof of an elementary property of generalized Lucas polynomials, inspired by [1]. These polynomials in s and t are defined by the recurrence relation 〈n〉 = s〈n-1〉+t〈n-2〉 for n ≥ 2. The initial values are 〈0〉 = 2; 〈1〉= s, respectively.
Some experience of shielding calculations by combinatorial method
International Nuclear Information System (INIS)
Korobejnikov, V.V.; Oussanov, V.I.
1996-01-01
Some aspects of the compound systems shielding calculations by a combinatorial approach are discussed. The effectiveness of such an approach is based on the fundamental characteristic of a compound system: if some element of the system have in itself mathematical or physical properties favorable for calculation, these properties may be used in a combinatorial approach and are lost when the system is being calculated in the whole by a direct approach. The combinatorial technique applied is well known. A compound system are being splitting for two or more auxiliary subsystems (so that calculation each of them is a more simple problem than calculation of the original problem (or at last is a soluble problem if original one is not). Calculation of every subsystem are carried out by suitable method and code, the coupling being made through boundary conditions or boundary source. The special consideration in the paper is given to a fast reactor shielding combinatorial analysis and to the testing of the results received. (author)
A combinatorial approximation algorithm for CDMA downlink rate allocation
Boucherie, Richardus J.; Bumb, A.F.; Endrayanto, A.I.; Woeginger, Gerhard; Raghavan, S.; Anandalingam, G.
2006-01-01
This paper presents a combinatorial algorithm for downlink rate allocation in Code Division Multiple Access (CDMA) mobile networks. By discretizing the coverage area into small segments, the transmit power requirements are characterized via a matrix representation that separates user and system
A combinatorial approximation algorithm for CDMA downlink rate allocation
Boucherie, Richardus J.; Bumb, A.F.; Endrayanto, A.I.; Woeginger, Gerhard
2004-01-01
This paper presents a combinatorial algorithm for downlink rate allocation in Code Division Multiple Access (CDMA) mobile networks. By discretizing the coverage area into small segments, the transmit power requirements are characterized via a matrix representation that separates user and system
A combinatorial enumeration problem of RNA secondary structures
African Journals Online (AJOL)
use
2011-12-21
Dec 21, 2011 ... interesting combinatorial questions (Chen et al., 2005;. Liu, 2006; Schmitt and Waterman 1994; Stein and. Waterman 1978). The research on the enumeration of. RNA secondary structures becomes one of the hot topics in Computational Molecular Biology. An RNA molecule is described by its sequences of.
Combinatorial nanodiamond in pharmaceutical and biomedical applications.
Lim, Dae Gon; Prim, Racelly Ena; Kim, Ki Hyun; Kang, Eunah; Park, Kinam; Jeong, Seong Hoon
2016-11-30
One of the newly emerging carbon materials, nanodiamond (ND), has been exploited for use in traditional electric materials and this has extended into biomedical and pharmaceutical applications. Recently, NDs have attained significant interests as a multifunctional and combinational drug delivery system. ND studies have provided insights into granting new potentials with their wide ranging surface chemistry, complex formation with biopolymers, and combination with biomolecules. The studies that have proved ND inertness, biocompatibility, and low toxicity have made NDs much more feasible for use in real in vivo applications. This review gives an understanding of NDs in biomedical engineering and pharmaceuticals, focusing on the classified introduction of ND/drug complexes. In addition, the diverse potential applications that can be obtained with chemical modification are presented. Copyright © 2016 Elsevier B.V. All rights reserved.
Neurogenetic Algorithm for Solving Combinatorial Engineering Problems
Directory of Open Access Journals (Sweden)
M. Jalali Varnamkhasti
2012-01-01
Full Text Available Diversity of the population in a genetic algorithm plays an important role in impeding premature convergence. This paper proposes an adaptive neurofuzzy inference system genetic algorithm based on sexual selection. In this technique, for choosing the female chromosome during sexual selection, a bilinear allocation lifetime approach is used to label the chromosomes based on their fitness value which will then be used to characterize the diversity of the population. The motivation of this algorithm is to maintain the population diversity throughout the search procedure. To promote diversity, the proposed algorithm combines the concept of gender and age of individuals and the fuzzy logic during the selection of parents. In order to appraise the performance of the techniques used in this study, one of the chemistry problems and some nonlinear functions available in literature is used.
Buncel, Erwin
2015-01-01
This book introduces the concepts, theory and experimental knowledge concerning solvent effects on the rate and equilibrium of chemical reactions of all kinds. It begins with basic thermodynamics and kinetics, building on this foundation to demonstrate how a more detailed understanding of these effects may be used to aid in determination of reaction mechanisms, and to aid in planning syntheses. Consideration is given to theoretical calculations (quantum chemistry, molecular dynamics, etc.), to statistical methods (chemometrics), and to modern day concerns such as ""green"" chemistry, where ut
Wang, Chen; Yang, Haowei; Tian, Li; Wang, Shiqiang; Gao, Ning; Zhang, Wanlin; Wang, Peng; Yin, Xianpeng; Li, Guangtao
2017-06-01
A three-dimensional (3D) inverse opal with periodic and porous structures has shown great potential for applications not only in optics and optoelectronics, but also in functional membranes. In this work, the benzaldehyde group was initially introduced into a 3D nanoporous inverse opal, serving as a platform for fabricating functional membranes. By employing the dynamic covalent approach, a highly controllable gating system was facilely fabricated to achieve modulable and reversible transport features. It was found that the physical/chemical properties and pore size of the gating system could easily be regulated through post-modification with amines. As a demonstration, the gated nanopores were modified with three kinds of amines to control the wettability, surface charge and nanopore size which in turn was exploited to achieve selective mass transport, including hydrophobic molecules, cations and anions, and the transport with respect to the physical steric hindrance. In particular, the gating system showed extraordinary reversibility and could recover to its pristine state by simply changing pH values. Due to the unlimited variety provided by the Schiff base reaction, the inverse opal described here exhibits a significant extendibility and could be easily post-modified with stimuli-responsive molecules for special purposes. Furthermore, this work can be extended to employ other dynamic covalent routes, for example Diels-Alder, ester exchange and disulfide exchange-based routes.
Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins.
Arvola, René M; Weidmann, Chase A; Tanaka Hall, Traci M; Goldstrohm, Aaron C
2017-11-02
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of 3 Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurologic processes. Here we synthesize 30 y of research with new insights into their molecular functions and mechanisms of action. First, we provide an overview of the key properties of each RBP. Next, we present a detailed analysis of their collaborative regulatory mechanism using a classic example of the developmental morphogen, hunchback, which is spatially and temporally regulated by the trio during embryogenesis. New biochemical, structural and functional analyses provide insights into RNA recognition, cooperativity, and regulatory mechanisms. We integrate these data into a model of combinatorial RNA binding and regulation of translation and mRNA decay. We then use this information, transcriptome wide analyses and bioinformatics predictions to assess the global impact of Pumilio, Nanos and Brain Tumor on gene regulation. Together, the results support pervasive, dynamic post-transcriptional control.
Paths and partitions: Combinatorial descriptions of the parafermionic states
Mathieu, Pierre
2009-09-01
The Zk parafermionic conformal field theories, despite the relative complexity of their modes algebra, offer the simplest context for the study of the bases of states and their different combinatorial representations. Three bases are known. The classic one is given by strings of the fundamental parafermionic operators whose sequences of modes are in correspondence with restricted partitions with parts at distance k -1 differing at least by 2. Another basis is expressed in terms of the ordered modes of the k -1 different parafermionic fields, which are in correspondence with the so-called multiple partitions. Both types of partitions have a natural (Bressoud) path representation. Finally, a third basis, formulated in terms of different paths, is inherited from the solution of the restricted solid-on-solid model of Andrews-Baxter-Forrester. The aim of this work is to review, in a unified and pedagogical exposition, these four different combinatorial representations of the states of the Zk parafermionic models. The first part of this article presents the different paths and partitions and their bijective relations; it is purely combinatorial, self-contained, and elementary; it can be read independently of the conformal-field-theory applications. The second part links this combinatorial analysis with the bases of states of the Zk parafermionic theories. With the prototypical example of the parafermionic models worked out in detail, this analysis contributes to fix some foundations for the combinatorial study of more complicated theories. Indeed, as we briefly indicate in ending, generalized versions of both the Bressoud and the Andrews-Baxter-Forrester paths emerge naturally in the description of the minimal models.
Balestrini, Raffaella; Polesello, Stefano; Sacchi, Elisa
2014-07-01
We monitored the chemical and isotopic compositions of wet depositions, at the Pyramid International Laboratory (5050 ma.s.l.), and surrounding surface waters, in the Khumbu basin, to understand precipitation chemistry and to obtain insights regarding ecosystem responses to atmospheric inputs. The major cations in the precipitation were NH4(+) and Ca(2+), whereas the main anion was HCO3(-), which constituted approximately 69% of the anions, followed by NO3(-), SO4(2-) and Cl(-). Data analysis suggested that Na(+), Cl(-) and K(+) were derived from the long-range transport of marine aerosols. Ca(2+), Mg(2+) and HCO3(-) were related to rock and soil dust contributions and the NO3(-) and SO4(2-) concentrations were derived from anthropogenic sources. Furthermore, NH4(+) was derived from gaseous NH3 scavenging. The isotopic composition of weekly precipitation ranged from -1.9 to -23.2‰ in δ(18)O, and from -0.8 to -174‰ in δ(2)H, with depleted values characterizing the central part of the monsoon period. The chemical composition of the stream water was dominated by calcite and/or gypsum dissolution. However, the isotopic composition of the stream water did not fully reflect the composition of the monsoon precipitation, which suggested that other water sources contributed to the stream flow. Precipitation contents for all ions were the lowest ones among those measured in high elevation sites around the world. During the monsoon periods the depositions were not substantially influenced by anthropogenic inputs, while in pre- and post-monsoon seasons the Himalayas could not represent an effective barrier for airborne pollution. In the late monsoon phase, the increase of ionic contents in precipitation could also be due to a change in the moisture source. The calculated atmospheric N load (0.30 kg ha(-1) y(-1)) was considerably lower than the levels that were measured in other high-altitude environments. Nevertheless, the NO3(-) concentrations in the surface waters
Lowe, John P
1993-01-01
Praised for its appealing writing style and clear pedagogy, Lowe's Quantum Chemistry is now available in its Second Edition as a text for senior undergraduate- and graduate-level chemistry students. The book assumes little mathematical or physical sophistication and emphasizes an understanding of the techniques and results of quantum chemistry, thus enabling students to comprehend much of the current chemical literature in which quantum chemical methods or concepts are used as tools. The book begins with a six-chapter introduction of standard one-dimensional systems, the hydrogen atom,
Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu
2017-07-28
Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO 2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S 0 ) state following electronic excitation to the S 1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S 1 to the S 0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S 1 state to the S 0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S 1 state to the ground S 0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.
Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu
2017-07-01
Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S0) state following electronic excitation to the S1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S1 to the S0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S1 state to the S0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S1 state to the ground S0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.
Phthalocyanine-loaded graphene nanoplatform for imaging-guided combinatorial phototherapy
Directory of Open Access Journals (Sweden)
Taratula O
2015-03-01
Full Text Available Olena Taratula,1 Mehulkumar Patel,2 Canan Schumann,1 Michael A Naleway,1 Addison J Pang,1 Huixin He,2 Oleh Taratula1 1Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR, USA; 2Department of Chemistry, Rutgers University-Newark, Newark, NJ, USA Abstract: We report a novel cancer-targeted nanomedicine platform for imaging and prospect for future treatment of unresected ovarian cancer tumors by intraoperative multimodal phototherapy. To develop the required theranostic system, novel low-oxygen graphene nanosheets were chemically modified with polypropylenimine dendrimers loaded with phthalocyanine (Pc as a photosensitizer. Such a molecular design prevents fluorescence quenching of the Pc by graphene nanosheets, providing the possibility of fluorescence imaging. Furthermore, the developed nanoplatform was conjugated with poly(ethylene glycol, to improve biocompatibility, and with luteinizing hormone-releasing hormone (LHRH peptide, for tumor-targeted delivery. Notably, a low-power near-infrared (NIR irradiation of single wavelength was used for both heat generation by the graphene nanosheets (photothermal therapy [PTT] and for reactive oxygen species (ROS-production by Pc (photodynamic therapy [PDT]. The combinatorial phototherapy resulted in an enhanced destruction of ovarian cancer cells, with a killing efficacy of 90%–95% at low Pc and low-oxygen graphene dosages, presumably conferring cytotoxicity to the synergistic effects of generated ROS and mild hyperthermia. An animal study confirmed that Pc loaded into the nanoplatform can be employed as a NIR fluorescence agent for imaging-guided drug delivery. Hence, the newly developed Pc-graphene nanoplatform has the significant potential as an effective NIR theranostic probe for imaging and combinatorial phototherapy. Keywords: graphene nanosheets, phthalocyanine, photothermal therapy, photodynamic therapy, theranostic
Fahlman, Bradley D
2011-01-01
The 2nd edition of Materials Chemistry builds on the strengths that were recognized by a 2008 Textbook Excellence Award from the Text and Academic Authors Association (TAA). Materials Chemistry addresses inorganic-, organic-, and nano-based materials from a structure vs. property treatment, providing a suitable breadth and depth coverage of the rapidly evolving materials field. The 2nd edition continues to offer innovative coverage and practical perspective throughout. After briefly defining materials chemistry and its history, seven chapters discuss solid-state chemistry, metals, semiconducting materials, organic "soft" materials, nanomaterials, and materials characterization. All chapters have been thoroughly updated and expanded with, for example, new sections on ‘soft lithographic’ patterning, ‘click chemistry’ polymerization, nanotoxicity, graphene, as well as many biomaterials applications. The polymer and ‘soft’ materials chapter represents the largest expansion for the 2nd edition. Each ch...
Energy Technology Data Exchange (ETDEWEB)
Choi, Jae Seong
1993-02-15
This book is comprised of nineteen chapters, which describes introduction of analytical chemistry, experimental error and statistics, chemistry equilibrium and solubility, gravimetric analysis with mechanism of precipitation, range and calculation of the result, volume analysis on general principle, sedimentation method on types and titration curve, acid base balance, acid base titration curve, complex and firing reaction, introduction of chemical electro analysis, acid-base titration curve, electrode and potentiometry, electrolysis and conductometry, voltammetry and polarographic spectrophotometry, atomic spectrometry, solvent extraction, chromatograph and experiments.
International Nuclear Information System (INIS)
Choi, Jae Seong
1993-02-01
This book is comprised of nineteen chapters, which describes introduction of analytical chemistry, experimental error and statistics, chemistry equilibrium and solubility, gravimetric analysis with mechanism of precipitation, range and calculation of the result, volume analysis on general principle, sedimentation method on types and titration curve, acid base balance, acid base titration curve, complex and firing reaction, introduction of chemical electro analysis, acid-base titration curve, electrode and potentiometry, electrolysis and conductometry, voltammetry and polarographic spectrophotometry, atomic spectrometry, solvent extraction, chromatograph and experiments.
Energy Technology Data Exchange (ETDEWEB)
Chae, Myeong Hu; Lee, Hu Jun; Kim, Ha Seok
1989-02-15
This book give explanations on analytical chemistry with ten chapters, which deal with development of analytical chemistry, the theory of error with definition and classification, sample and treatment gravimetry on general process of gravimetry in aqueous solution and non-aqueous solution, precipitation titration about precipitation reaction and types, complexometry with summary and complex compound, oxidation-reduction equilibrium on electrode potential and potentiometric titration, solvent extraction and chromatograph and experiment with basic operation for chemical experiment.
International Nuclear Information System (INIS)
Chae, Myeong Hu; Lee, Hu Jun; Kim, Ha Seok
1989-02-01
This book give explanations on analytical chemistry with ten chapters, which deal with development of analytical chemistry, the theory of error with definition and classification, sample and treatment gravimetry on general process of gravimetry in aqueous solution and non-aqueous solution, precipitation titration about precipitation reaction and types, complexometry with summary and complex compound, oxidation-reduction equilibrium on electrode potential and potentiometric titration, solvent extraction and chromatograph and experiment with basic operation for chemical experiment.
Energy Technology Data Exchange (ETDEWEB)
Collison, Melanie
2011-05-15
Green chemistry is the science of chemistry used in a way that will not use or create hazardous substances. Dr. Rui Resendes is working in this field at GreenCentre Canada, an offshoot of PARTEQ Innovations in Kingston, Ontario. GreenCentre's preliminary findings suggest their licensed product {sup S}witchable Solutions{sup ,} featuring 3 classes of solvents and a surfactant, may be useful in bitumen oil sands extraction.
Simsek, Yusuf; Brown, Alex
2018-05-09
Molecular dynamic (MD) simulations were carried out to obtain the conformational changes of the chromophore in the gold fluorescent protein (PDB ID: 1OXF). To obtain two-photon absorption (TPA) cross-sections, time dependent density functional theory (TD-DFT) computations were performed for chromophore geometries sampled along the trajectory. The TD-DFT computations used the CAM-B3LYP functional and 6-31+G(d) basis set with the conductor-like polarizable continuum model (PCM) with parameters for water. Results showed that two dihedral angles change remarkably over the simulation time. TPA cross-sections were found to average 20 GM for the excitation to S1 between 430 and 460 nm; however, the maximal and minimal values were 35GM and 5GM, respectively. Besides the effects of the dihedrals on the spectroscopic properties, some bond lengths affected the excitation energies and the TPA cross-sections significantly (up to ±25-30%) while the effects of bond angles were smaller (±5%). Overall the present results provide insight in the effects of conformational exibility on TPA (with gold fluorescent protein as a specific example) and suggest that further experimental measurements of TPA for gold fluorescent protein should be undertaken.
International Nuclear Information System (INIS)
Krantzman, K.D.; Kingsbury, D.B.; Garrison, Barbara J.
2007-01-01
Molecular dynamics simulations of the sputtering of Si by keV C 60 bombardment have been performed as a function of incident kinetic energy at two incident angles, normal incidence and 45 deg. Nearly all of the C atoms remain embedded in the surface after bombardment because the C atoms from the projectile form strong covalent bonds with the Si atoms in the target. At low incident kinetic energies, the sputtering yield of Si atoms is small and there is a net deposition of solid material from the projectile atoms. As the incident kinetic energy is increased, the yield of sputtered Si atoms increases. A transition occurs in which the yield of sputtered Si atoms exceeds the number of C atoms deposited, and there is a net erosion of the solid material. A significantly higher sputter yield is observed at an incident angle of 45 deg. than at normal incidence, and therefore, the energy value is lower for the transition from net deposition to net erosion. This phenomenon is discussed in terms of the depth distribution of deposited energy, which is found to be shallower at an incident angle of 45 deg
Ninth international symposium on hot atom chemistry. Abstracts
International Nuclear Information System (INIS)
1977-01-01
Abstracts of the papers presented at the Symposium are compiled. The topics considered were chemical dynamics of high energy reactions, hot atom chemistry in organic compounds of tritium, nitrogen, oxygen, and halogens, theory and chemical dynamics of hot atom reactions as determined by beam studies, solid state reactions of recoil atoms and implanted ions, hot atom chemistry in energy-related research, hot atom chemistry in inorganic compounds of oxygen and tritium, hot positronium chemistry, applied hot atom chemistry in labelling, chemical effects of radioactive decay, decay-induced reactions and excitation labelling, physical methods in hot atom chemistry, and hot atom reactions in radiation and stratospheric chemistry
Energy Technology Data Exchange (ETDEWEB)
Kabius, Bernd C.; Browning, Nigel D.; Thevuthasan, Suntharampillai; Diehl, Barbara L.; Stach, Eric A.
2012-07-25
This report summarizes a 2011 workshop that addressed the potential role of rapid, time-resolved electron microscopy measurements in accelerating the solution of important scientific and technical problems. A series of U.S. Department of Energy (DOE) and National Academy of Science workshops have highlighted the critical role advanced research tools play in addressing scientific challenges relevant to biology, sustainable energy, and technologies that will fuel economic development without degrading our environment. Among the specific capability needs for advancing science and technology are tools that extract more detailed information in realistic environments (in situ or operando) at extreme conditions (pressure and temperature) and as a function of time (dynamic and time-dependent). One of the DOE workshops, Future Science Needs and Opportunities for Electron Scattering: Next Generation Instrumentation and Beyond, specifically addressed the importance of electron-based characterization methods for a wide range of energy-relevant Grand Scientific Challenges. Boosted by the electron optical advancement in the last decade, a diversity of in situ capabilities already is available in many laboratories. The obvious remaining major capability gap in electron microscopy is in the ability to make these direct in situ observations over a broad spectrum of fast (µs) to ultrafast (picosecond [ps] and faster) temporal regimes. In an effort to address current capability gaps, EMSL, the Environmental Molecular Sciences Laboratory, organized an Ultrafast Electron Microscopy Workshop, held June 14-15, 2011, with the primary goal to identify the scientific needs that could be met by creating a facility capable of a strongly improved time resolution with integrated in situ capabilities. The workshop brought together more than 40 leading scientists involved in applying and/or advancing electron microscopy to address important scientific problems of relevance to DOE’s research
Combinatorial and computational mathematics present and future
Hong, Sungpyo; Kim, Ki Hang; Roush, Fred W
2001-01-01
This book describes and summarizes past work in important areas of combinatorics and computation, as well as gives directions for researchers working in these areas in the 21st century. It contains primarily survey papers and presents original research by Peter Fishburn, Jim Ho Kwak, Jaeun Lee, K H Kim, F W Roush and Susan Williams. The papers deal with some of the most exciting and promising developments in the areas of coding theory in relation to number theory, lattice theory and its applications, graph theory and its applications, topological techniques in combinatorics, symbolic dynamics
Programme for test generation for combinatorial and sequential systems
International Nuclear Information System (INIS)
Tran Huy Hoan
1973-01-01
This research thesis reports the computer-assisted search for tests aimed at failure detection in combinatorial and sequential logic circuits. As he wants to deal with complex circuits with many modules such as those met in large scale integrated circuits (LSI), the author used propagation paths. He reports the development of a method which is valid for combinatorial systems and for several sequential circuits comprising elementary logic modules and JK and RS flip-flops. This method is developed on an IBM 360/91 computer in PL/1 language. The used memory space is limited and adjustable with respect to circuit dimension. Computing time is short when compared to that needed by other programmes. The solution is practical and efficient for failure test and localisation
Bioinspired computation in combinatorial optimization: algorithms and their computational complexity
DEFF Research Database (Denmark)
Neumann, Frank; Witt, Carsten
2012-01-01
Bioinspired computation methods, such as evolutionary algorithms and ant colony optimization, are being applied successfully to complex engineering and combinatorial optimization problems, and it is very important that we understand the computational complexity of these algorithms. This tutorials...... problems. Classical single objective optimization is examined first. They then investigate the computational complexity of bioinspired computation applied to multiobjective variants of the considered combinatorial optimization problems, and in particular they show how multiobjective optimization can help...... to speed up bioinspired computation for single-objective optimization problems. The tutorial is based on a book written by the authors with the same title. Further information about the book can be found at www.bioinspiredcomputation.com....
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Ravasi, Timothy; Suzuki, Harukazu; Cannistraci, Carlo; Katayama, Shintaro; Bajic, Vladimir B.; Tan, Kai; Akalin, Altuna; Schmeier, Sebastian; Kanamori-Katayama, Mutsumi; Bertin, Nicolas; Carninci, Piero; Daub, Carsten O.; Forrest, Alistair R.R.; Gough, Julian; Grimmond, Sean; Han, Jung-Hoon; Hashimoto, Takehiro; Hide, Winston; Hofmann, Oliver; Kamburov, Atanas; Kaur, Mandeep; Kawaji, Hideya; Kubosaki, Atsutaka; Lassmann, Timo; van Nimwegen, Erik; MacPherson, Cameron Ross; Ogawa, Chihiro; Radovanovic, Aleksandar; Schwartz, Ariel; Teasdale, Rohan D.; Tegné r, Jesper; Lenhard, Boris; Teichmann, Sarah A.; Arakawa, Takahiro; Ninomiya, Noriko; Murakami, Kayoko; Tagami, Michihira; Fukuda, Shiro; Imamura, Kengo; Kai, Chikatoshi; Ishihara, Ryoko; Kitazume, Yayoi; Kawai, Jun; Hume, David A.; Ideker, Trey; Hayashizaki, Yoshihide
2010-01-01
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
CUNY Graduate Center Workshops on Combinatorial and Additive Number Theory
2017-01-01
Based on talks from the 2015 and 2016 Combinatorial and Additive Number Theory (CANT) workshops at the City University of New York, these proceedings offer 19 peer-reviewed and edited papers on current topics in number theory. Held every year since 2003, the workshop series surveys state-of-the-art open problems in combinatorial and additive number theory and related parts of mathematics. Sumsets, partitions, convex polytopes and discrete geometry, Ramsey theory, primality testing, and cryptography are among the topics featured in this volume. Each contribution is dedicated to a specific topic that reflects the latest results by experts in the field. Researchers and graduate students interested in the current progress in number theory will find this selection of articles relevant and compelling. .
Combinatorial geometry domain decomposition strategies for Monte Carlo simulations
Energy Technology Data Exchange (ETDEWEB)
Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z. [Institute of Applied Physics and Computational Mathematics, Beijing, 100094 (China)
2013-07-01
Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)
Combinatorial geometry domain decomposition strategies for Monte Carlo simulations
International Nuclear Information System (INIS)
Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z.
2013-01-01
Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)
Laguerre-type derivatives: Dobinski relations and combinatorial identities
International Nuclear Information System (INIS)
Penson, K. A.; Blasiak, P.; Horzela, A.; Duchamp, G. H. E.; Solomon, A. I.
2009-01-01
We consider properties of the operators D(r,M)=a r (a † a) M (which we call generalized Laguerre-type derivatives), with r=1,2,..., M=0,1,..., where a and a † are boson annihilation and creation operators, respectively, satisfying [a,a † ]=1. We obtain explicit formulas for the normally ordered form of arbitrary Taylor-expandable functions of D(r,M) with the help of an operator relation that generalizes the Dobinski formula. Coherent state expectation values of certain operator functions of D(r,M) turn out to be generating functions of combinatorial numbers. In many cases the corresponding combinatorial structures can be explicitly identified.
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Ravasi, Timothy
2010-03-01
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
Combinatorial Optimization in Project Selection Using Genetic Algorithm
Dewi, Sari; Sawaluddin
2018-01-01
This paper discusses the problem of project selection in the presence of two objective functions that maximize profit and minimize cost and the existence of some limitations is limited resources availability and time available so that there is need allocation of resources in each project. These resources are human resources, machine resources, raw material resources. This is treated as a consideration to not exceed the budget that has been determined. So that can be formulated mathematics for objective function (multi-objective) with boundaries that fulfilled. To assist the project selection process, a multi-objective combinatorial optimization approach is used to obtain an optimal solution for the selection of the right project. It then described a multi-objective method of genetic algorithm as one method of multi-objective combinatorial optimization approach to simplify the project selection process in a large scope.
Non-unique factorizations algebraic, combinatorial and analytic theory
Geroldinger, Alfred
2006-01-01
From its origins in algebraic number theory, the theory of non-unique factorizations has emerged as an independent branch of algebra and number theory. Focused efforts over the past few decades have wrought a great number and variety of results. However, these remain dispersed throughout the vast literature. For the first time, Non-Unique Factorizations: Algebraic, Combinatorial, and Analytic Theory offers a look at the present state of the theory in a single, unified resource.Taking a broad look at the algebraic, combinatorial, and analytic fundamentals, this book derives factorization results and applies them in concrete arithmetical situations using appropriate transfer principles. It begins with a basic introduction that can be understood with knowledge of standard basic algebra. The authors then move to the algebraic theory of monoids, arithmetic theory of monoids, the structure of sets of lengths, additive group theory, arithmetical invariants, and the arithmetic of Krull monoids. They also provide a s...
Combinatorial nuclear level density by a Monte Carlo method
International Nuclear Information System (INIS)
Cerf, N.
1994-01-01
We present a new combinatorial method for the calculation of the nuclear level density. It is based on a Monte Carlo technique, in order to avoid a direct counting procedure which is generally impracticable for high-A nuclei. The Monte Carlo simulation, making use of the Metropolis sampling scheme, allows a computationally fast estimate of the level density for many fermion systems in large shell model spaces. We emphasize the advantages of this Monte Carlo approach, particularly concerning the prediction of the spin and parity distributions of the excited states,and compare our results with those derived from a traditional combinatorial or a statistical method. Such a Monte Carlo technique seems very promising to determine accurate level densities in a large energy range for nuclear reaction calculations
Hartwig, Sonja; Czibere, Akos; Kotzka, Jorg; Passlack, Waltraud; Haas, Rainer; Eckel, Jürgen; Lehr, Stefan
2009-07-01
Blood serum samples are the major source for clinical proteomics approaches, which aim to identify diagnostically relevant or treatment-response related proteins. But, the presence of very high-abundance proteins and the enormous dynamic range of protein distribution hinders whole serum analysis. An innovative tool to overcome these limitations, utilizes combinatorial hexapeptide ligand libraries (ProteoMiner). Here, we demonstrate that ProteoMiner can be used for comparative and quantitative analysis of complex proteomes. We spiked serum samples with increasing amounts (3 microg to 300 microg) of whole E. coli lysate, processed it with ProteoMiner and performed quantitative analyses of 2D-gels. We found, that the concentration of the spiked bacteria proteome, reflected by the maintained proportional spot intensities, was not altered by ProteoMiner treatment. Therefore, we conclude that the ProteoMiner technology can be used for quantitative analysis of low abundant proteins in complex biological samples.
Quantum mechanics in chemistry
Schatz, George C
2002-01-01
Intended for graduate and advanced undergraduate students, this text explores quantum mechanical techniques from the viewpoint of chemistry and materials science. Dynamics, symmetry, and formalism are emphasized. An initial review of basic concepts from introductory quantum mechanics is followed by chapters examining symmetry, rotations, and angular momentum addition. Chapter 4 introduces the basic formalism of time-dependent quantum mechanics, emphasizing time-dependent perturbation theory and Fermi's golden rule. Chapter 5 sees this formalism applied to the interaction of radiation and matt
Obfuscation Framework Based on Functionally Equivalent Combinatorial Logic Families
2008-03-01
of Defense, or the United States Government . AFIT/GCS/ENG/08-12 Obfuscation Framework Based on Functionally Equivalent Combinatorial Logic Families...time, United States policy strongly encourages the sale and transfer of some military equipment to foreign governments and makes it easier for...Proceedings of the International Conference on Availability, Reliability and Security, 2007. 14. McDonald, J. Todd and Alec Yasinsac. “Of unicorns and random
Combinatorial drug screening identifies Ewing sarcoma-specific sensitivities
Radic-Sarikas, Branka; Tsafou, Kalliopi P.; Emdal, Kristina B.; Papamarkou, Theodore; Huber, Kilian V.M.; Mutz, Cornelia; Toretsky, Jeffrey A.; Bennett, Keiryn L.; Olsen, Jesper V.; Brunak, Søren; Kovar, Heinrich; Superti-Furga, Giulio
2017-01-01
Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three p...
Rapid mapping of protein functional epitopes by combinatorial alanine scanning
Weiss, GA; Watanabe, CK; Zhong, A; Goddard, A; Sidhu, SS
2000-01-01
A combinatorial alanine-scanning strategy was used to determine simultaneously the functional contributions of 19 side chains buried at the interface between human growth hormone and the extracellular domain of its receptor. A phage-displayed protein library was constructed in which the 19 side chains were preferentially allowed to vary only as the wild type or alanine. The library pool was subjected to binding selections to isolate functional clones, and DNA sequencing was used to determine ...
Combinatorial Models for Assembly and Decomposition of Products
A. N. Bojko
2015-01-01
The paper discusses the most popular combinatorial models that are used for the synthesis of design solutions at the stage of the assembly process flow preparation. It shows that while assembling the product the relations of parts can be represented as a structure of preferences, which is formed on the basis of objective design restrictions put in at the stage of the product design. This structure is a binary preference relation pre-order. Its symmetrical part is equivalence and describes the...
From combinatorial optimization to real algebraic geometry and back
Directory of Open Access Journals (Sweden)
Janez Povh
2014-12-01
Full Text Available In this paper, we explain the relations between combinatorial optimization and real algebraic geometry with a special focus to the quadratic assignment problem. We demonstrate how to write a quadratic optimization problem over discrete feasible set as a linear optimization problem over the cone of completely positive matrices. The latter formulation enables a hierarchy of approximations which rely on results from polynomial optimization, a sub-eld of real algebraic geometry.
A binary plasmid system for shuffling combinatorial antibody libraries.
Collet, T A; Roben, P; O'Kennedy, R; Barbas, C F; Burton, D R; Lerner, R A
1992-01-01
We have used a binary system of replicon-compatible plasmids to test the potential for promiscuous recombination of heavy and light chains within sets of human Fab fragments isolated from combinatorial antibody libraries. Antibody molecules showed a surprising amount of promiscuity in that a particular heavy chain could recombine with multiple light chains with retention of binding to a protein antigen. The degree to which a given heavy chain productively paired with any light chain to bind a...
Distributing the computation in combinatorial optimization experiments over the cloud
Directory of Open Access Journals (Sweden)
Mario Brcic
2017-12-01
Full Text Available Combinatorial optimization is an area of great importance since many of the real-world problems have discrete parameters which are part of the objective function to be optimized. Development of combinatorial optimization algorithms is guided by the empirical study of the candidate ideas and their performance over a wide range of settings or scenarios to infer general conclusions. Number of scenarios can be overwhelming, especially when modeling uncertainty in some of the problem’s parameters. Since the process is also iterative and many ideas and hypotheses may be tested, execution time of each experiment has an important role in the efficiency and successfulness. Structure of such experiments allows for significant execution time improvement by distributing the computation. We focus on the cloud computing as a cost-efficient solution in these circumstances. In this paper we present a system for validating and comparing stochastic combinatorial optimization algorithms. The system also deals with selection of the optimal settings for computational nodes and number of nodes in terms of performance-cost tradeoff. We present applications of the system on a new class of project scheduling problem. We show that we can optimize the selection over cloud service providers as one of the settings and, according to the model, it resulted in a substantial cost-savings while meeting the deadline.
View discovery in OLAP databases through statistical combinatorial optimization
Energy Technology Data Exchange (ETDEWEB)
Hengartner, Nick W [Los Alamos National Laboratory; Burke, John [PNNL; Critchlow, Terence [PNNL; Joslyn, Cliff [PNNL; Hogan, Emilie [PNNL
2009-01-01
OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of 'views' of an OLAP database as a combinatorial object of all projections and subsets, and 'view discovery' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline 'hop-chaining' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a 'spiraling' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.
A combinatorial perspective of the protein inference problem.
Yang, Chao; He, Zengyou; Yu, Weichuan
2013-01-01
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to facilitate the identification of proteins from peptide identification results. However, the relationship between protein identification and peptide identification has not been thoroughly explained before. In this paper, we devote ourselves to a combinatorial perspective of the protein inference problem. We employ combinatorial mathematics to calculate the conditional protein probabilities (protein probability means the probability that a protein is correctly identified) under three assumptions, which lead to a lower bound, an upper bound, and an empirical estimation of protein probabilities, respectively. The combinatorial perspective enables us to obtain an analytical expression for protein inference. Our method achieves comparable results with ProteinProphet in a more efficient manner in experiments on two data sets of standard protein mixtures and two data sets of real samples. Based on our model, we study the impact of unique peptides and degenerate peptides (degenerate peptides are peptides shared by at least two proteins) on protein probabilities. Meanwhile, we also study the relationship between our model and ProteinProphet. We name our program ProteinInfer. Its Java source code, our supplementary document and experimental results are available at: >http://bioinformatics.ust.hk/proteininfer.
View Discovery in OLAP Databases through Statistical Combinatorial Optimization
Energy Technology Data Exchange (ETDEWEB)
Joslyn, Cliff A.; Burke, Edward J.; Critchlow, Terence J.
2009-05-01
The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of ``views'' of an OLAP database as a combinatorial object of all projections and subsets, and ``view discovery'' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline ``hop-chaining'' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a ``spiraling'' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.
Quantum Adiabatic Optimization and Combinatorial Landscapes
Smelyanskiy, V. N.; Knysh, S.; Morris, R. D.
2003-01-01
In this paper we analyze the performance of the Quantum Adiabatic Evolution (QAE) algorithm on a variant of Satisfiability problem for an ensemble of random graphs parametrized by the ratio of clauses to variables, gamma = M / N. We introduce a set of macroscopic parameters (landscapes) and put forward an ansatz of universality for random bit flips. We then formulate the problem of finding the smallest eigenvalue and the excitation gap as a statistical mechanics problem. We use the so-called annealing approximation with a refinement that a finite set of macroscopic variables (verses only energy) is used, and are able to show the existence of a dynamic threshold gamma = gammad, beyond which QAE should take an exponentially long time to find a solution. We compare the results for extended and simplified sets of landscapes and provide numerical evidence in support of our universality ansatz.
Piot, M.; Pay, M. T.; Jorba, O.; Baldasano, J. M.; Jiménez-Guerrero, P.; López, E.; Pérez, C.; Gassó, S.
2009-04-01
Often in Europe, population exposure to air pollution exceeds standards set by the EU and the World Health Organization (WHO). Urban/suburban areas are predominantly impacted upon, although exceedances of particulate matter (PM10 and PM2.5) and Ozone (O3) also take place in rural areas. In the frame of the CALIOPE project (Baldasano et al., 2008a), a high-resolution air quality forecasting system, WRF-ARW/HERMES/CMAQ/DREAM, has been developed and applied to the European domain (12km x 12km, 1hr) as well as to the Iberian Peninsula domain (4km x 4km, 1hr) to provide air quality forecasts for Spain (http://www.bsc.es/caliope/). The simulation of such high-resolution model system has been made possible by its implementation on the MareNostrum supercomputer. To reassure potential users and reduce uncertainties, the model system must be evaluated to assess its performances in terms of air quality levels and dynamics reproducibility. The present contribution describes a thorough quantitative evaluation study performed for a reference year (2004). The CALIOPE modelling system is configured with 38 vertical layers reaching up to 50 hPa for the meteorological core. Atmospheric initial and boundary conditions are obtained from the NCEP final analysis data. The vertical resolution of the CMAQ chemistry-transport model for gas-phase and aerosols has been increased from 8 to 15 layers in order to simulate vertical exchanges more accurately. Gas phase boundary conditions are provided by the LMDz-INCA2 global climate-chemistry model (see Hauglustaine et al., 2004). The DREAM model simulates long-range transport of mineral dust over the domains under study. For the European simulation, emissions are disaggregated from the EMEP expert emission inventory for 2004 to the utilized resolution using the criteria implemented in the HERMES emission model (Baldasano et al., 2008b). The HERMES model system, using a bottom-up approach, was adopted to estimate emissions for the Iberian
Loeffler, Felix F; Foertsch, Tobias C; Popov, Roman; Mattes, Daniela S; Schlageter, Martin; Sedlmayr, Martyna; Ridder, Barbara; Dang, Florian-Xuan; von Bojničić-Kninski, Clemens; Weber, Laura K; Fischer, Andrea; Greifenstein, Juliane; Bykovskaya, Valentina; Buliev, Ivan; Bischoff, F Ralf; Hahn, Lothar; Meier, Michael A R; Bräse, Stefan; Powell, Annie K; Balaban, Teodor Silviu; Breitling, Frank; Nesterov-Mueller, Alexander
2016-06-14
Laser writing is used to structure surfaces in many different ways in materials and life sciences. However, combinatorial patterning applications are still limited. Here we present a method for cost-efficient combinatorial synthesis of very-high-density peptide arrays with natural and synthetic monomers. A laser automatically transfers nanometre-thin solid material spots from different donor slides to an acceptor. Each donor bears a thin polymer film, embedding one type of monomer. Coupling occurs in a separate heating step, where the matrix becomes viscous and building blocks diffuse and couple to the acceptor surface. Furthermore, we can consecutively deposit two material layers of activation reagents and amino acids. Subsequent heat-induced mixing facilitates an in situ activation and coupling of the monomers. This allows us to incorporate building blocks with click chemistry compatibility or a large variety of commercially available non-activated, for example, posttranslationally modified building blocks into the array's peptides with >17,000 spots per cm(2).
Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried
2015-01-01
A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis. PMID:26355961
International Nuclear Information System (INIS)
Kwon, Yeong Sik; Lee, Dong Seop; Ryu, Haung Ryong; Jang, Cheol Hyeon; Choi, Bong Jong; Choi, Sang Won
1993-07-01
The book concentrates on the latest general chemistry, which is divided int twenty-three chapters. It deals with basic conception and stoichiometry, nature of gas, structure of atoms, quantum mechanics, symbol and structure of an electron of ion and molecule, chemical thermodynamics, nature of solid, change of state and liquid, properties of solution, chemical equilibrium, solution and acid-base, equilibrium of aqueous solution, electrochemistry, chemical reaction speed, molecule spectroscopy, hydrogen, oxygen and water, metallic atom; 1A, IIA, IIIA, carbon and atom IVA, nonmetal atom and an inert gas, transition metals, lanthanons, and actinoids, nuclear properties and radioactivity, biochemistry and environment chemistry.
International Nuclear Information System (INIS)
Swallow, A.J.
1983-01-01
The subject is covered in chapters, entitled: introduction (defines scope of article as dealing with the chemistry of reactive species, (e.g. excess electrons, excited states, free radicals and inorganic ions in unusual valency states) as studied using radiation with radiation chemistry in its traditional sense and with biological and industrial applications); gases; water and simple inorganic systems; aqueous metallo-organic compounds and metalloproteins; small organic molecules in aqueous solution; microheterogeneous systems; non-aqueous liquids and solutions; solids; biological macromolecules; synthetic polymers. (U.K.)
DEFF Research Database (Denmark)
Weschler, Charles J.; Carslaw, Nicola
2018-01-01
This review aims to encapsulate the importance, ubiquity, and complexity of indoor chemistry. We discuss the many sources of indoor air pollutants and summarize their chemical reactions in the air and on surfaces. We also summarize some of the known impacts of human occupants, who act as sources...... and sinks of indoor chemicals, and whose activities (e.g., cooking, cleaning, smoking) can lead to extremely high pollutant concentrations. As we begin to use increasingly sensitive and selective instrumentation indoors, we are learning more about chemistry in this relatively understudied environment....
Alencar, Wagner S; Crespilho, Frank N; Martins, Marccus V A; Zucolotto, Valtencir; Oliveira, Osvaldo N; Silva, Welter C
2009-07-07
The concept of constitutional dynamic chemistry (CDC) based on the control of non-covalent interactions in supramolecular structures is promising for having a large impact on nanoscience and nanotechnology if adequate nanoscale manipulation methods are used. In this study, we demonstrate that the layer-by-layer (LbL) technique may be used to produce electroactive electrodes with ITO coated by tetrasulfonated nickel phthalocyanine (NiTsPc) alternated with poly(allylamine hydrochloride) (PAH) incorporating gold nanoparticles (AuNP), in which synergy has been achieved in the interaction between the nanoparticles and NiTsPc. The catalytic activity toward hydrogen peroxide (H(2)O(2)) in multilayer films was investigated using cyclic voltammetry, where oxidation of H(2)O(2) led to increased currents in the PAH-AuNP/NiTsPc films for the electrochemical processes associated with the phthalocyanine ring and nickel at 0.52 and 0.81 V vs. SCE, respectively, while for PAH/NiTsPc films (without AuNP) only the first redox process was affected. In control experiments we found out that the catalytic activity was not solely due to the presence of AuNP, but rather to the nanoparticles inducing NiTsPc supramolecular structures that favored access to their redox sites, thus yielding strong charge transfer. The combined effects of NiTsPc and AuNP, which could only be observed in nanostructured LbL films, point to another avenue to pursue within the CDC paradigm.
The Pictet-Spengler reaction in solid-phase combinatorial chemistry
DEFF Research Database (Denmark)
Nielsen, Thomas E; Diness, Frederik; Meldal, Morten
2003-01-01
The Pictet-Spengler reaction is an important reaction for the generation of tetrahydro-beta-carbolines and tetrahydroisoquinoline ring systems, which exhibit a range of biological and pharmacological properties. This review covers the solid-phase Pictet-Spengler reaction, as employed in solid...
Handbook of heterocyclic chemistry
National Research Council Canada - National Science Library
Katritzky, Alan R
2010-01-01
... Heterocyclic Chemistry I (1984) Comprehensive Heterocyclic Chemistry II (1996) Comprehensive Heterocyclic Chemistry III (2008) Comprehensive Organic Functional Group Transformations I (1995) Compreh...
Fang, Guanghua; Xue, Mengzhu; Su, Mingbo; Hu, Dingyu; Li, Yanlian; Xiong, Bing; Ma, Lanping; Meng, Tao; Chen, Yuelei; Li, Jingya; Li, Jia; Shen, Jingkang
2012-07-15
The introduction of the multi-objective optimization has dramatically changed the virtual combinatorial library design, which can consider many objectives simultaneously, such as synthesis cost and drug-likeness, thus may increase positive rates of biological active compounds. Here we described a software called CCLab (Combinatorial Chemistry Laboratory) for combinatorial library design based on the multi-objective genetic algorithm. Tests of the convergence ability and the ratio to re-take the building blocks in the reference library were conducted to assess the software in silico, and then it was applied to a real case of designing a 5×6 HDAC inhibitor library. Sixteen compounds in the resulted library were synthesized, and the histone deactetylase (HDAC) enzymatic assays proved that 14 compounds showed inhibitory ratios more than 50% against tested 3 HDAC enzymes at concentration of 20 μg/mL, with IC(50) values of 3 compounds comparable to SAHA. These results demonstrated that the CCLab software could enhance the hit rates of the designed library and would be beneficial for medicinal chemists to design focused library in drug development (the software can be downloaded at: http://202.127.30.184:8080/drugdesign.html). Copyright © 2012 Elsevier Ltd. All rights reserved.
Whitesides, George McClelland
2015-01-01
Chemistry is in a period of change, from an era focused on molecules and reactions, to one in which manipulations of systems of molecules and reactions will be essential parts of controlling larger systems. This Essay traces paths from the past to possible futures.
School Science Review, 1972
1972-01-01
Short articles on the kinetics of the hydrogen peroxide-iodide ion reaction, simulation of fluidization catalysis, the use of Newman projection diagrams to represent steric relationships in organic chemistry, the use of synthetic substrates for proteolytic enzyme reactions, and two simple clock reactions"--hydrolysis of halogenoalkanes and…
Piot, M.; Pay, M.; Jorba, O.; Lopez, E.; Pirez, C.; Gasso, S.; Baldasano, J. M.
2009-12-01
In Europe, human exposure to air pollution often exceeds standards set by the EU commission (Directives 1996/62/EC, 2002/3/EC, 2008/50/EC) and the World Health Organization (WHO). Urban/suburban areas are predominantly impacted upon, although exceedances of particulate matter (PM10 and PM2.5) and Ozone (O3) also take place in rural areas. Within the CALIOPE project, a high-resolution air quality forecasting system, namely WRF-ARW/HERMES04/CMAQ/BSC-DREAM, has been developed and applied to the European domain (12x12 sq. km, 1hr) as well as the Spanish domain (4x4 sq. km, 1hr). The simulation of such high-resolution model system has been made possible by its implementation on the MareNostrum supercomputer. This contribution describes a thorough quantitative evaluation study performed for the reference year 2004. The WRF-ARW meteorological model contains 38 vertical layers reaching up to 50 hPa. The vertical resolution of the CMAQ chemistry-transport model for gas-phase and aerosols has been increased from 8 to 15 layers in order to simulate vertical exchanges more accurately. Gas phase boundary conditions are provided by the LMDz-INCA2 global climate-chemistry model. For the European simulation, emissions are disaggregated from the EMEP emission inventory for 2004 to the utilized resolution using the criteria implemented in the HERMES04 emission model. The HERMES04 model system, running through a bottom-up approach, is used to estimate emissions for Spain at a 1x1 sq. km horizontal resolution, every hour. In order to evaluate the performances of the CALIOPE system, the model simulation for Europe was compared with ground-based measurements from the EMEP and the Spanish air quality networks (total of 60 stations for O3, 43 for NO2, 31 for SO2, 25 for PM10 and 16 for PM2.5). The model simulation for Europe satisfactorily reproduces O3 concentrations throughout the year (annual correlation: 0.66) with relatively small errors: MNGE values range from 13% to 26%, and MNBE
International Nuclear Information System (INIS)
Broerse, J.J.; Barendsen, G.W.; Kal, H.B.; Kogel, A.J. van der
1983-01-01
This book contains the extended abstracts of the contributions of the poster workshop sessions on chemistry and physics of the 7th international congress of radiation research. They cover the following main topics: primary processes in radiation physics and chemistry, general chemistry in radiation chemistry, DNA and model systems in radiation chemistry, molecules of biological interest in radiation chemistry, techniques in radiation chemistry, hot atom chemistry. refs.; figs.; tabs
International Nuclear Information System (INIS)
Laszlo, P.
1988-01-01
The 1988 progress report of the Fine Chemistry laboratory (Polytechnic School, France) is presented. The research programs are centered on the renewal of the organic chemistry most important reactions and on the invention of new, highly efficient and highly selective reactions, by applying low cost reagents and solvents. An important research domain concerns the study and fabrication of new catalysts. They are obtained by means of the reactive sputtering of the metals and metal oxydes thin films. The Monte Carlo simulations of the long-range electrostatic interaction in a clay and the obtention of acrylamides from anhydrous or acrylic ester are summarized. Moreover, the results obtained in the field of catalysis are also given. The published papers and the congress communications are included [fr
International Nuclear Information System (INIS)
1982-01-01
The bibliography of Hungarian literature in the field of radioanalytical chemistry covers the four-year period 1976-1979. The list of papers contains 290 references in the alphabetical order of the first authors. The majority of the titles belongs to neutron activation analysis, labelling, separation and determination of radioactive isotopes. Other important fields like radioimmunoassay, environmental protection etc. are covered as well. (Sz.J.)
International Nuclear Information System (INIS)
Anon.
1985-01-01
The division for Analytical Chemistry continued to try and develope an accurate method for the separation of trace amounts from mixtures which, contain various other elements. Ion exchange chromatography is of special importance in this regard. New separation techniques were tried on certain trace amounts in South African standard rock materials and special ceramics. Methods were also tested for the separation of carrier-free radioisotopes from irradiated cyclotron discs
Industrial chemistry engineering
International Nuclear Information System (INIS)
1993-01-01
This book on industrial chemistry engineering is divided in two parts. The first part deals with industrial chemistry, inorganic industrial chemistry, organic industrial chemistry, analytical chemistry and practical questions. The last parts explain the chemical industry, a unit parts and thermodynamics in chemical industry and reference. It reveals the test subjects for the industrial chemistry engineering with a written examination and practical skill.
Arnold, J. O.
1987-01-01
With the advent of supercomputers, modern computational chemistry algorithms and codes, a powerful tool was created to help fill NASA's continuing need for information on the properties of matter in hostile or unusual environments. Computational resources provided under the National Aerodynamics Simulator (NAS) program were a cornerstone for recent advancements in this field. Properties of gases, materials, and their interactions can be determined from solutions of the governing equations. In the case of gases, for example, radiative transition probabilites per particle, bond-dissociation energies, and rates of simple chemical reactions can be determined computationally as reliably as from experiment. The data are proving to be quite valuable in providing inputs to real-gas flow simulation codes used to compute aerothermodynamic loads on NASA's aeroassist orbital transfer vehicles and a host of problems related to the National Aerospace Plane Program. Although more approximate, similar solutions can be obtained for ensembles of atoms simulating small particles of materials with and without the presence of gases. Computational chemistry has application in studying catalysis, properties of polymers, all of interest to various NASA missions, including those previously mentioned. In addition to discussing these applications of computational chemistry within NASA, the governing equations and the need for supercomputers for their solution is outlined.
International Nuclear Information System (INIS)
Warner, John C.; Cannon, Amy S.; Dye, Kevin M.
2004-01-01
A grand challenge facing government, industry, and academia in the relationship of our technological society to the environment is reinventing the use of materials. To address this challenge, collaboration from an interdisciplinary group of stakeholders will be necessary. Traditionally, the approach to risk management of materials and chemicals has been through inerventions intended to reduce exposure to materials that are hazardous to health and the environment. In 1990, the Pollution Prevention Act encouraged a new tact-elimination of hazards at the source. An emerging approach to this grand challenge seeks to embed the diverse set of environmental perspectives and interests in the everyday practice of the people most responsible for using and creating new materials--chemists. The approach, which has come to be known as Green Chemistry, intends to eliminate intrinsic hazard itself, rather than focusing on reducing risk by minimizing exposure. This chapter addresses the representation of downstream environmental stakeholder interests in the upstream everyday practice that is reinventing chemistry and its material inputs, products, and waste as described in the '12 Principles of Green Chemistry'
Combinatorial effects of arginine and fluoride on oral bacteria.
Zheng, X; Cheng, X; Wang, L; Qiu, W; Wang, S; Zhou, Y; Li, M; Li, Y; Cheng, L; Li, J; Zhou, X; Xu, X
2015-02-01
Dental caries is closely associated with the microbial disequilibrium between acidogenic/aciduric pathogens and alkali-generating commensal residents within the dental plaque. Fluoride is a widely used anticaries agent, which promotes tooth hard-tissue remineralization and suppresses bacterial activities. Recent clinical trials have shown that oral hygiene products containing both fluoride and arginine possess a greater anticaries effect compared with those containing fluoride alone, indicating synergy between fluoride and arginine in caries management. Here, we hypothesize that arginine may augment the ecological benefit of fluoride by enriching alkali-generating bacteria in the plaque biofilm and thus synergizes with fluoride in controlling dental caries. Specifically, we assessed the combinatory effects of NaF/arginine on planktonic and biofilm cultures of Streptococcus mutans, Streptococcus sanguinis, and Porphyromonas gingivalis with checkerboard microdilution assays. The optimal NaF/arginine combinations were selected, and their combinatory effects on microbial composition were further examined in single-, dual-, and 3-species biofilm using bacterial species-specific fluorescence in situ hybridization and quantitative polymerase chain reaction. We found that arginine synergized with fluoride in suppressing acidogenic S. mutans in both planktonic and biofilm cultures. In addition, the NaF/arginine combination synergistically reduced S. mutans but enriched S. sanguinis within the multispecies biofilms. More importantly, the optimal combination of NaF/arginine maintained a "streptococcal pressure" against the potential growth of oral anaerobe P. gingivalis within the alkalized biofilm. Taken together, we conclude that the combinatory application of fluoride and arginine has a potential synergistic effect in maintaining a healthy oral microbial equilibrium and thus represents a promising ecological approach to caries management. © International & American
Atmosphere physics and chemistry
International Nuclear Information System (INIS)
Delmas, R.; Megie, G.; Peuch, V.H.
2005-10-01
Since the 1970's, the awareness about the atmospheric pollution threat has led to a spectacular development of the researches on the complex interactions between the chemical composition of the atmosphere and the climate. This book makes a synthesis of the state-of-the-art in this very active domain of research. Content: introduction, atmosphere dynamics and transport, matter-radiation interaction and radiant transfer, physico-chemical processes, atmospheric aerosol and heterogenous chemistry, anthropic and natural emissions and deposition, stratospheric chemical system, tropospheric chemical system, polluted boundary layer, paleo-environments and ice archives, role of atmospheric chemistry in global changes, measurement principles and instruments, numerical modeling, experimental strategy, regulation and management of the atmospheric environment, index. (J.S.)
Combinatorial interpretations of binomial coefficient analogues related to Lucas sequences
Sagan, Bruce; Savage, Carla
2009-01-01
Let s and t be variables. Define polynomials {n} in s, t by {0}=0, {1}=1, and {n}=s{n-1}+t{n-2} for n >= 2. If s, t are integers then the corresponding sequence of integers is called a Lucas sequence. Define an analogue of the binomial coefficients by C{n,k}={n}!/({k}!{n-k}!) where {n}!={1}{2}...{n}. It is easy to see that C{n,k} is a polynomial in s and t. The purpose of this note is to give two combinatorial interpretations for this polynomial in terms of statistics on integer partitions in...
First steps in combinatorial optimization on graphons: matchings
Czech Academy of Sciences Publication Activity Database
Doležal, Martin; Hladký, J.; Hu, P.; Piguet, Diana
2017-01-01
Roč. 61, August (2017), s. 359-365 ISSN 1571-0653 R&D Projects: GA ČR GA16-07378S; GA ČR GJ16-07822Y EU Projects: European Commission(XE) 628974 - PAECIDM Institutional support: RVO:67985840 ; RVO:67985807 Keywords : graphon * graph limits * matching * combinatorial optimization Subject RIV: BA - General Mathematics ; BA - General Mathematics (UIVT-O) OBOR OECD: Pure mathematics ; Pure mathematics (UIVT-O) http://www.sciencedirect.com/science/article/pii/S1571065317301452
Combinatorial synthesis of oxazol-thiazole bis-heterocyclic compounds.
Murru, Siva; Nefzi, Adel
2014-01-13
A combinatorial library of novel oxazol-thiazole bis-heterocycles was synthesized in good to excellent overall yields with high purity using a solution and solid-phase parallel synthesis approach. Oxazole amino acids, prepared from serine methyl ester and amino acids via coupling and cyclodehydration, were treated with Fmoc-NCS and α-haloketones for the parallel synthesis of diverse bis-heterocycles. Fmoc-isothiocyanate is used as a traceless reagent for thiazole formation. Oxazole diversity can be achieved by using variety of amino acids, whereas thiazole diversity is produced with various haloketones.
Advances in bio-inspired computing for combinatorial optimization problems
Pintea, Camelia-Mihaela
2013-01-01
Advances in Bio-inspired Combinatorial Optimization Problems' illustrates several recent bio-inspired efficient algorithms for solving NP-hard problems.Theoretical bio-inspired concepts and models, in particular for agents, ants and virtual robots are described. Large-scale optimization problems, for example: the Generalized Traveling Salesman Problem and the Railway Traveling Salesman Problem, are solved and their results are discussed.Some of the main concepts and models described in this book are: inner rule to guide ant search - a recent model in ant optimization, heterogeneous sensitive a
Proceedings of the 8th Nordic Combinatorial Conference
DEFF Research Database (Denmark)
Geil, Olav; Andersen, Lars Døvling
The Nordic Combinatorial Conferences were initiated in 1981 by mathematicians from Stavanger. Held approximately every three years since then, the conferences have been able to sustain the interest from combinatorialists all over the Nordic countries. In 2004 the 8th conference is held in Aalborg......, Denmark. We are pleased that so many people have chosen to attend, and that lectures were offered from more participants than we had originally reserved time for. We asked two mathematicians to give special lectures and are happy that both accepted immediately. Andries Brouwer from the Technical...
Combinatorial interpretation of Haldane-Wu fractional exclusion statistics.
Aringazin, A K; Mazhitov, M I
2002-08-01
Assuming that the maximal allowed number of identical particles in a state is an integer parameter, q, we derive the statistical weight and analyze the associated equation that defines the statistical distribution. The derived distribution covers Fermi-Dirac and Bose-Einstein ones in the particular cases q=1 and q--> infinity (n(i)/q-->1), respectively. We show that the derived statistical weight provides a natural combinatorial interpretation of Haldane-Wu fractional exclusion statistics, and present exact solutions of the distribution equation.
What Diagrams Argue in Late Imperial Chinese Combinatorial Texts.
Bréard, Andrea
2015-01-01
Attitudes towards diagrammatic reasoning and visualization in mathematics were seldom spelled out in texts from pre-modern China, although illustrations figure prominently in mathematical literature since the eleventh century. Taking the sums of finite series and their combinatorial interpretation as a case study, this article investigates the epistemological function of illustrations from the eleventh to the nineteenth century that encode either the mathematical objects themselves or represent their related algorithms. It particularly focuses on the two illustrations given in Wang Lai's (1768-1813) Mathematical Principles of Sequential Combinations, arguing that they reflect a specific mode of nineteenth-century mathematical argumentative practice and served as a heuristic model for later authors.
Design of diversity and focused combinatorial libraries in drug discovery.
Young, S Stanley; Ge, Nanxiang
2004-05-01
Using well-characterized chemical reactions and readily available monomers, chemists are able to create sets of compounds, termed libraries, which are useful in drug discovery processes. The design of combinatorial chemical libraries can be complex and there has been much information recently published offering suggestions on how the design process can be carried out. This review focuses on literature with the goal of organizing current thinking. At this point in time, it is clear that benchmarking of current suggested methods is required as opposed to further new methods.
First steps in combinatorial optimization on graphons: matchings
Czech Academy of Sciences Publication Activity Database
Doležal, Martin; Hladký, J.; Hu, P.; Piguet, Diana
2017-01-01
Roč. 61, August (2017), s. 359-365 ISSN 1571-0653 R&D Projects: GA ČR GA16-07378S; GA ČR GJ16-07822Y EU Projects: European Commission(XE) 628974 - PAECIDM Institutional support: RVO:67985840 ; RVO:67985807 Keywords : graphon * graph limits * matching * combinatorial optimization Subject RIV: BA - General Mathematics; BA - General Mathematics (UIVT-O) OBOR OECD: Pure mathematics; Pure mathematics (UIVT-O) http://www.sciencedirect.com/science/article/pii/S1571065317301452
LOGICAL REASONING ABILITY AND STUDENT PERFORMANCE IN GENERAL CHEMISTRY.
Bird, Lillian
2010-03-01
Logical reasoning skills of students enrolled in General Chemistry at the University of Puerto Rico in Río Piedras were measured using the Group Assessment of Logical Thinking (GALT) test. The results were used to determine the students' cognitive level (concrete, transitional, formal) as well as their level of performance by logical reasoning mode (mass/volume conservation, proportional reasoning, correlational reasoning, experimental variable control, probabilistic reasoning and combinatorial reasoning). This information was used to identify particular deficiencies and gender effects, and to determine which logical reasoning modes were the best predictors of student performance in the general chemistry course. Statistical tests to analyze the relation between (a) operational level and final grade in both semesters of the course; (b) GALT test results and performance in the ACS General Chemistry Examination; and (c) operational level and student approach (algorithmic or conceptual) towards a test question that may be answered correctly using either strategy, were also performed.
Enumeration of Combinatorial Classes of Single Variable Complex Polynomial Vector Fields
DEFF Research Database (Denmark)
Dias, Kealey
A vector field in the space of degree d monic, centered single variable complex polynomial vector fields has a combinatorial structure which can be fully described by a combinatorial data set consisting of an equivalence relation and a marked subset on the integers mod 2d-2, satisfying certain...
Validation of an Instrument and Testing Protocol for Measuring the Combinatorial Analysis Schema.
Staver, John R.; Harty, Harold
1979-01-01
Designs a testing situation to examine the presence of combinatorial analysis, to establish construct validity in the use of an instrument, Combinatorial Analysis Behavior Observation Scheme (CABOS), and to investigate the presence of the schema in young adolescents. (Author/GA)
International Nuclear Information System (INIS)
Azmy, Y. Y.
2004-01-01
An approach is developed for solving the neutron diffusion equation on combinatorial geometry computational cells, that is computational cells composed by combinatorial operations involving simple-shaped component cells. The only constraint on the component cells from which the combinatorial cells are assembled is that they possess a legitimate discretization of the underlying diffusion equation. We use the Finite Difference (FD) approximation of the x, y-geometry diffusion equation in this work. Performing the same combinatorial operations involved in composing the combinatorial cell on these discrete-variable equations yields equations that employ new discrete variables defined only on the combinatorial cell's volume and faces. The only approximation involved in this process, beyond the truncation error committed in discretizing the diffusion equation over each component cell, is a consistent-order Legendre series expansion. Preliminary results for simple configurations establish the accuracy of the solution to the combinatorial geometry solution compared to straight FD as the system dimensions decrease. Furthermore numerical results validate the consistent Legendre-series expansion order by illustrating the second order accuracy of the combinatorial geometry solution, the same as standard FD. Nevertheless the magnitude of the error for the new approach is larger than FD's since it incorporates the additional truncated series approximation. (authors)
An Investigation into Post-Secondary Students' Understanding of Combinatorial Questions
Bulone, Vincent William
2017-01-01
The purpose of this dissertation was to study aspects of how post-secondary students understand combinatorial problems. Within this dissertation, I considered understanding through two different lenses: i) student connections to previous problems; and ii) common combinatorial distinctions such as ordered versus unordered and repetitive versus…
Wieberger, Florian; Kolb, Tristan; Neuber, Christian; Ober, Christopher K; Schmidt, Hans-Werner
2013-04-08
In this article we present several developed and improved combinatorial techniques to optimize processing conditions and material properties of organic thin films. The combinatorial approach allows investigations of multi-variable dependencies and is the perfect tool to investigate organic thin films regarding their high performance purposes. In this context we develop and establish the reliable preparation of gradients of material composition, temperature, exposure, and immersion time. Furthermore we demonstrate the smart application of combinations of composition and processing gradients to create combinatorial libraries. First a binary combinatorial library is created by applying two gradients perpendicular to each other. A third gradient is carried out in very small areas and arranged matrix-like over the entire binary combinatorial library resulting in a ternary combinatorial library. Ternary combinatorial libraries allow identifying precise trends for the optimization of multi-variable dependent processes which is demonstrated on the lithographic patterning process. Here we verify conclusively the strong interaction and thus the interdependency of variables in the preparation and properties of complex organic thin film systems. The established gradient preparation techniques are not limited to lithographic patterning. It is possible to utilize and transfer the reported combinatorial techniques to other multi-variable dependent processes and to investigate and optimize thin film layers and devices for optical, electro-optical, and electronic applications.
Directory of Open Access Journals (Sweden)
Hans-Werner Schmidt
2013-04-01
Full Text Available In this article we present several developed and improved combinatorial techniques to optimize processing conditions and material properties of organic thin films. The combinatorial approach allows investigations of multi-variable dependencies and is the perfect tool to investigate organic thin films regarding their high performance purposes. In this context we develop and establish the reliable preparation of gradients of material composition, temperature, exposure, and immersion time. Furthermore we demonstrate the smart application of combinations of composition and processing gradients to create combinatorial libraries. First a binary combinatorial library is created by applying two gradients perpendicular to each other. A third gradient is carried out in very small areas and arranged matrix-like over the entire binary combinatorial library resulting in a ternary combinatorial library. Ternary combinatorial libraries allow identifying precise trends for the optimization of multi-variable dependent processes which is demonstrated on the lithographic patterning process. Here we verify conclusively the strong interaction and thus the interdependency of variables in the preparation and properties of complex organic thin film systems. The established gradient preparation techniques are not limited to lithographic patterning. It is possible to utilize and transfer the reported combinatorial techniques to other multi-variable dependent processes and to investigate and optimize thin film layers and devices for optical, electro-optical, and electronic applications.
Combinatorial therapy discovery using mixed integer linear programming.
Pang, Kaifang; Wan, Ying-Wooi; Choi, William T; Donehower, Lawrence A; Sun, Jingchun; Pant, Dhruv; Liu, Zhandong
2014-05-15
Combinatorial therapies play increasingly important roles in combating complex diseases. Owing to the huge cost associated with experimental methods in identifying optimal drug combinations, computational approaches can provide a guide to limit the search space and reduce cost. However, few computational approaches have been developed for this purpose, and thus there is a great need of new algorithms for drug combination prediction. Here we proposed to formulate the optimal combinatorial therapy problem into two complementary mathematical algorithms, Balanced Target Set Cover (BTSC) and Minimum Off-Target Set Cover (MOTSC). Given a disease gene set, BTSC seeks a balanced solution that maximizes the coverage on the disease genes and minimizes the off-target hits at the same time. MOTSC seeks a full coverage on the disease gene set while minimizing the off-target set. Through simulation, both BTSC and MOTSC demonstrated a much faster running time over exhaustive search with the same accuracy. When applied to real disease gene sets, our algorithms not only identified known drug combinations, but also predicted novel drug combinations that are worth further testing. In addition, we developed a web-based tool to allow users to iteratively search for optimal drug combinations given a user-defined gene set. Our tool is freely available for noncommercial use at http://www.drug.liuzlab.org/. zhandong.liu@bcm.edu Supplementary data are available at Bioinformatics online.
Causal gene identification using combinatorial V-structure search.
Cai, Ruichu; Zhang, Zhenjie; Hao, Zhifeng
2013-07-01
With the advances of biomedical techniques in the last decade, the costs of human genomic sequencing and genomic activity monitoring are coming down rapidly. To support the huge genome-based business in the near future, researchers are eager to find killer applications based on human genome information. Causal gene identification is one of the most promising applications, which may help the potential patients to estimate the risk of certain genetic diseases and locate the target gene for further genetic therapy. Unfortunately, existing pattern recognition techniques, such as Bayesian networks, cannot be directly applied to find the accurate causal relationship between genes and diseases. This is mainly due to the insufficient number of samples and the extremely high dimensionality of the gene space. In this paper, we present the first practical solution to causal gene identification, utilizing a new combinatorial formulation over V-Structures commonly used in conventional Bayesian networks, by exploring the combinations of significant V-Structures. We prove the NP-hardness of the combinatorial search problem under a general settings on the significance measure on the V-Structures, and present a greedy algorithm to find sub-optimal results. Extensive experiments show that our proposal is both scalable and effective, particularly with interesting findings on the causal genes over real human genome data. Copyright © 2013 Elsevier Ltd. All rights reserved.
A combinatorial approach to diffeomorphism invariant quantum gauge theories
International Nuclear Information System (INIS)
Zapata, J.A.
1997-01-01
Quantum gauge theory in the connection representation uses functions of holonomies as configuration observables. Physical observables (gauge and diffeomorphism invariant) are represented in the Hilbert space of physical states; physical states are gauge and diffeomorphism invariant distributions on the space of functions of the holonomies of the edges of a certain family of graphs. Then a family of graphs embedded in the space manifold (satisfying certain properties) induces a representation of the algebra of physical observables. We construct a quantum model from the set of piecewise linear graphs on a piecewise linear manifold, and another manifestly combinatorial model from graphs defined on a sequence of increasingly refined simplicial complexes. Even though the two models are different at the kinematical level, they provide unitarily equivalent representations of the algebra of physical observables in separable Hilbert spaces of physical states (their s-knot basis is countable). Hence, the combinatorial framework is compatible with the usual interpretation of quantum field theory. copyright 1997 American Institute of Physics
A combinatorial approach to the design of vaccines.
Martínez, Luis; Milanič, Martin; Legarreta, Leire; Medvedev, Paul; Malaina, Iker; de la Fuente, Ildefonso M
2015-05-01
We present two new problems of combinatorial optimization and discuss their applications to the computational design of vaccines. In the shortest λ-superstring problem, given a family S1,...,S(k) of strings over a finite alphabet, a set Τ of "target" strings over that alphabet, and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ target strings as substrings of S(i). In the shortest λ-cover superstring problem, given a collection X1,...,X(n) of finite sets of strings over a finite alphabet and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ elements of X(i) as substrings. The two problems are polynomially equivalent, and the shortest λ-cover superstring problem is a common generalization of two well known combinatorial optimization problems, the shortest common superstring problem and the set cover problem. We present two approaches to obtain exact or approximate solutions to the shortest λ-superstring and λ-cover superstring problems: one based on integer programming, and a hill-climbing algorithm. An application is given to the computational design of vaccines and the algorithms are applied to experimental data taken from patients infected by H5N1 and HIV-1.
Device for preparing combinatorial libraries in powder metallurgy.
Yang, Shoufeng; Evans, Julian R G
2004-01-01
This paper describes a powder-metering, -mixing, and -dispensing mechanism that can be used as a method for producing large numbers of samples for metallurgical evaluation or electrical or mechanical testing from multicomponent metal and cermet powder systems. It is designed to make use of the same commercial powders that are used in powder metallurgy and, therefore, to produce samples that are faithful to the microstructure of finished products. The particle assemblies produced by the device could be consolidated by die pressing, isostatic pressing, laser sintering, or direct melting. The powder metering valve provides both on/off and flow rate control of dry powders in open capillaries using acoustic vibration. The valve is simple and involves no relative movement, avoiding seizure with fine powders. An orchestra of such valves can be arranged on a building platform to prepare multicomponent combinatorial libraries. As with many combinatorial devices, identification and evaluation of sources of mixing error as a function of sample size is mandatory. Such an analysis is presented.
Dissection of combinatorial control by the Met4 transcriptional complex.
Lee, Traci A; Jorgensen, Paul; Bognar, Andrew L; Peyraud, Caroline; Thomas, Dominique; Tyers, Mike
2010-02-01
Met4 is the transcriptional activator of the sulfur metabolic network in Saccharomyces cerevisiae. Lacking DNA-binding ability, Met4 must interact with proteins called Met4 cofactors to target promoters for transcription. Two types of DNA-binding cofactors (Cbf1 and Met31/Met32) recruit Met4 to promoters and one cofactor (Met28) stabilizes the DNA-bound Met4 complexes. To dissect this combinatorial system, we systematically deleted each category of cofactor(s) and analyzed Met4-activated transcription on a genome-wide scale. We defined a core regulon for Met4, consisting of 45 target genes. Deletion of both Met31 and Met32 eliminated activation of the core regulon, whereas loss of Met28 or Cbf1 interfered with only a subset of targets that map to distinct sectors of the sulfur metabolic network. These transcriptional dependencies roughly correlated with the presence of Cbf1 promoter motifs. Quantitative analysis of in vivo promoter binding properties indicated varying levels of cooperativity and interdependency exists between members of this combinatorial system. Cbf1 was the only cofactor to remain fully bound to target promoters under all conditions, whereas other factors exhibited different degrees of regulated binding in a promoter-specific fashion. Taken together, Met4 cofactors use a variety of mechanisms to allow differential transcription of target genes in response to various cues.
A binary plasmid system for shuffling combinatorial antibody libraries.
Collet, T A; Roben, P; O'Kennedy, R; Barbas, C F; Burton, D R; Lerner, R A
1992-11-01
We have used a binary system of replicon-compatible plasmids to test the potential for promiscuous recombination of heavy and light chains within sets of human Fab fragments isolated from combinatorial antibody libraries. Antibody molecules showed a surprising amount of promiscuity in that a particular heavy chain could recombine with multiple light chains with retention of binding to a protein antigen. The degree to which a given heavy chain productively paired with any light chain to bind antigen varied from 43% to 100% and depended strongly on the heavy-chain sequence. Such productive crosses resulted in a set of Fab fragments of similar apparent binding constants, which seemed to differ mainly in the amount of active Fab fragment produced in the bacterial cell. The dominance of the heavy chain in the antibody-antigen interaction was further explored in a set of directed crosses, in which heavy and light chains derived from antigen-specific clones were crossed with nonrelated heavy and light chains. In these crosses, an Fab fragment retained antigen binding only if it contained a heavy chain from an antigen-specific clone. In no case did the light chain confer detectable affinity when paired with indifferent heavy chains. The surprising promiscuity of heavy chains has ramifications for the evaluation of the diversity of combinatorial libraries made against protein antigens and should allow the combination of one such promiscuous heavy chain with an engineered light chain to form an Fab fragment carrying synthetic cofactors to assist in antibody catalysis.
Theoretical chemistry periodicities in chemistry and biology
Eyring, Henry
1978-01-01
Theoretical Chemistry: Periodicities in Chemistry and Biology, Volume 4 covers the aspects of theoretical chemistry. The book discusses the stably rotating patterns of reaction and diffusion; the chemistry of inorganic systems exhibiting nonmonotonic behavior; and population cycles. The text also describes the mathematical modeling of excitable media in neurobiology and chemistry; oscillating enzyme reactions; and oscillatory properties and excitability of the heart cell membrane. Selected topics from the theory of physico-chemical instabilities are also encompassed. Chemists, mechanical engin
Energy Technology Data Exchange (ETDEWEB)
None
1973-07-01
Research progress is reported on studies in heavy element chemistry. Topics considered are: synergistic complexes of plutonyl ion; water uptake in synergistic systems; formation constants of some uranyl BETA -diketone complexes; thermodynamic acid dissociation constants of BETA -diketones; thermodynamic formation constants of uranyl BETA -diketonates; thiocyanate complexes of some trivalent lanthanides and actinides; stability constants of actinide complexes using dinonyl naphthalenesulfonic acid extraction; TBP extraction of actinides; stability constants of complexes of Pu(III) with 5- sulfosalicycllc acid; and solvent extraction behavior of Pu( VII). (DHM)
Klemperer, William
2006-08-15
In the past half century, radioastronomy has changed our perception and understanding of the universe. In this issue of PNAS, the molecular chemistry directly observed within the galaxy is discussed. For the most part, the description of the molecular transformations requires specific kinetic schemes rather than chemical thermodynamics. Ionization of the very abundant molecular hydrogen and atomic helium followed by their secondary reactions is discussed. The rich variety of organic species observed is a challenge for complete understanding. The role and nature of reactions involving grain surfaces as well as new spectroscopic observations of interstellar and circumstellar regions are topics presented in this special feature.
Learning Organic Chemistry Through Natural Products -12 ...
Indian Academy of Sciences (India)
Higher Learning. Generations of students would vouch for the fact that he has the uncanny ability to present the chemistry of natural products logically and with feeling. The most interesting chemical aspect of a molecule is its. reactivHy pattern. NR Krishnaswamy. In this part of the series, dynamic organic chemistry and.
Rehder, Dieter
2010-01-01
The dynamic field of extraterrestrial chemistry brings together ideas of chemistr, astrophysics, and biology to the study of molecules between stars, around stars, and on plantes. This book serves as an introduction to chemial processes under ?unearthly? and hence usually extreme conditions (temperature, pressure, high or low density, bombardment by cosmic rays), and their impact on the early development of our solar system, as well as providing a deeper understanding of processes in earthly regions where conditions approach those of extraterrestrial areas.A unique and extraordinary perspe
Eighteenth annual West Coast theoretical chemistry conference
Energy Technology Data Exchange (ETDEWEB)
NONE
1997-05-01
Abstracts are presented from the eighteenth annual west coast theoretical chemistry conference. Topics include molecular simulations; quasiclassical simulations of reactions; photodissociation reactions; molecular dynamics;interface studies; electronic structure; and semiclassical methods of reactive systems.
Radiation chemistry and bioradical chemistry
International Nuclear Information System (INIS)
Ferradini, C.
1991-01-01
Oxygen metabolism results, at the cellular level, in the formation of superoxyde radical O 2 - · and probably also of hydroxyl radical OH·. Other radical species can be produced from exogenous or endogenous molecules and nearly all of them have the possibility to react with oxygen giving peroxyradicals. Some of these transients play a role in various biological processes such as phagocytosis, inflammation or ischemy although the mechanisms invoked are poorly understood. Radiation chemistry is an invaluable tool for obtaining a quantitative view of these mechanisms. A description is given of this interaction [fr
Development of Combinatorial Methods for Alloy Design and Optimization
International Nuclear Information System (INIS)
Pharr, George M.; George, Easo P.; Santella, Michael L
2005-01-01
The primary goal of this research was to develop a comprehensive methodology for designing and optimizing metallic alloys by combinatorial principles. Because conventional techniques for alloy preparation are unavoidably restrictive in the range of alloy composition that can be examined, combinatorial methods promise to significantly reduce the time, energy, and expense needed for alloy design. Combinatorial methods can be developed not only to optimize existing alloys, but to explore and develop new ones as well. The scientific approach involved fabricating an alloy specimen with a continuous distribution of binary and ternary alloy compositions across its surface--an ''alloy library''--and then using spatially resolved probing techniques to characterize its structure, composition, and relevant properties. The three specific objectives of the project were: (1) to devise means by which simple test specimens with a library of alloy compositions spanning the range interest can be produced; (2) to assess how well the properties of the combinatorial specimen reproduce those of the conventionally processed alloys; and (3) to devise screening tools which can be used to rapidly assess the important properties of the alloys. As proof of principle, the methodology was applied to the Fe-Ni-Cr ternary alloy system that constitutes many commercially important materials such as stainless steels and the H-series and C-series heat and corrosion resistant casting alloys. Three different techniques were developed for making alloy libraries: (1) vapor deposition of discrete thin films on an appropriate substrate and then alloying them together by solid-state diffusion; (2) co-deposition of the alloying elements from three separate magnetron sputtering sources onto an inert substrate; and (3) localized melting of thin films with a focused electron-beam welding system. Each of the techniques was found to have its own advantages and disadvantages. A new and very powerful technique for
Fundamentals of nuclear chemistry
International Nuclear Information System (INIS)
Majer, K.
1982-01-01
The textbook is a Czech-to-German translation of the second revised edition and covers the subject under the headings: general nuclear chemistry, methods of nuclear chemistry, preparative nuclear chemistry, analytical nuclear chemistry, and applied chemistry. The book is especially directed to students
International Nuclear Information System (INIS)
Khan, M.Z.; Chuaqui, C.A.
1990-05-01
The chemistry of cyclodextrins was studied. This study included synthesising some cyclodextrin derivatives, preparing selected inclusion complexes with cyclodextrin and investigating the effects of gamma irradiation on cyclodextrins and certain linear oligosaccharides. This report presents a brief review of the structure and properties of cyclodextrins, the synthesis of cyclodextrin derivatives, their complexation and applications. This is followed by a description of the synthesis of some cyclodextrin derivatives and the preparation of inclusion complexes of cyclodextrin with some organic compounds. Finally, the effects of gamma irradiation on cyclodextrins, some of their derivatives and certain structurally related carbohydrates are discussed. The gamma irradiation studies were carried out for two reasons: to study the effects of gamma irradiation on cyclodextrins and their derivatives; and to investigate selectivity during the gamma irradiation of cyclodextrin derivatives
Klemperer, William
2011-01-01
The discovery of polar polyatomic molecules in higher-density regions of the interstellar medium by means of their rotational emission detected by radioastronomy has changed our conception of the universe from essentially atomic to highly molecular. We discuss models for molecule formation, emphasizing the general lack of thermodynamic equilibrium. Detailed chemical kinetics is needed to understand molecule formation as well as destruction. Ion molecule reactions appear to be an important class for the generally low temperatures of the interstellar medium. The need for the intrinsically high-quality factor of rotational transitions to definitively pin down molecular emitters has been well established by radioastronomy. The observation of abundant molecular ions both positive and, as recently observed, negative provides benchmarks for chemical kinetic schemes. Of considerable importance in guiding our understanding of astronomical chemistry is the fact that the larger molecules (with more than five atoms) are all organic.
Physical chemistry and the environment
International Nuclear Information System (INIS)
Dunning, T.H. Jr.; Garrett, B.C.; Kolb, C.E. Jr.; Shaw, R.W.; Choppin, G.R.; Wagner, A.F.
1994-08-01
From the ozone hole and the greenhouse effect to plastics recycling and hazardous waste disposal, society faces a number of issues, the solutions to which require an unprecedented understanding of the properties of molecules. We are coming to realize that the environment is a coupled set of chemical systems, its dynamics determining the welfare of the biosphere and of humans in particular. These chemical systems are governed by fundamental molecular interactions, and they present chemists with an unparalleled challenge. The application of current concepts of molecular behavior and of up-to-date experimental and computational techniques can provide us with insights into the environment that are needed to mitigate past damage, to anticipate the impact of current human activity, and to avoid future insults to the environment. Environmental chemistry encompasses a number of separate, yet interlocking, areas of research. In all of these areas progress is limited by an inadequate understanding of the underlying chemical processes involved. Participation of all chemical approaches -- experimental, theoretical and computational -- and of all disciplines of chemistry -- organic, inorganic, physical, analytical and biochemistry -- will be required to provide the necessary fundamental understanding. The Symposium on ''Physical Chemistry and the Environment'' was designed to bring the many exciting and challenging physical chemistry problems involved in environmental chemistry to the attention of a larger segment of the physical chemistry community
The construction of combinatorial manifolds with prescribed sets of links of vertices
International Nuclear Information System (INIS)
Gaifullin, A A
2008-01-01
To every oriented closed combinatorial manifold we assign the set (with repetitions) of isomorphism classes of links of its vertices. The resulting transformation L is the main object of study in this paper. We pose an inversion problem for L and show that this problem is closely related to Steenrod's problem on the realization of cycles and to the Rokhlin-Schwartz-Thom construction of combinatorial Pontryagin classes. We obtain a necessary condition for a set of isomorphism classes of combinatorial spheres to belong to the image of L. (Sets satisfying this condition are said to be balanced.) We give an explicit construction showing that every balanced set of isomorphism classes of combinatorial spheres falls into the image of L after passing to a multiple set and adding several pairs of the form (Z,-Z), where -Z is the sphere Z with the orientation reversed. Given any singular simplicial cycle ξ of a space X, this construction enables us to find explicitly a combinatorial manifold M and a map φ:M→X such that φ * [M]=r[ξ] for some positive integer r. The construction is based on resolving singularities of ξ. We give applications of the main construction to cobordisms of manifolds with singularities and cobordisms of simple cells. In particular, we prove that every rational additive invariant of cobordisms of manifolds with singularities admits a local formula. Another application is the construction of explicit (though inefficient) local combinatorial formulae for polynomials in the rational Pontryagin classes of combinatorial manifolds
Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities
DEFF Research Database (Denmark)
Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.
2017-01-01
Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...
Combinatorial study of zinc tin oxide thin-film transistors
McDowell, M. G.; Sanderson, R. J.; Hill, I. G.
2008-01-01
Groups of thin-film transistors using a zinc tin oxide semiconductor layer have been fabricated via a combinatorial rf sputtering technique. The ZnO :SnO2 ratio of the film varies as a function of position on the sample, from pure ZnO to SnO2, allowing for a study of zinc tin oxide transistor performance as a function of channel stoichiometry. The devices were found to have mobilities ranging from 2to12cm2/Vs, with two peaks in mobility in devices at ZnO fractions of 0.80±0.03 and 0.25±0.05, and on/off ratios as high as 107. Transistors composed predominantly of SnO2 were found to exhibit light sensitivity which affected both the on/off ratios and threshold voltages of these devices.