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Title:

Sticky triangles: New tools for experimental phasing of biological macromolecules

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X-ray crystallography is the prime method for the elucidation of three-dimensional molecular structures. It enables the structure determination of biological macromolecules such as proteins and nucleic acids. The determination of novel macromolecular structures is hampered by the crystallographic phase problem, i.e. only the intensity of the ref...

X-ray crystallography is the prime method for the elucidation of three-dimensional molecular structures. It enables the structure determination of biological macromolecules such as proteins and nucleic acids. The determination of novel macromolecular structures is hampered by the crystallographic phase problem, i.e. only the intensity of the reflections but not their phase angle can be recorded during the diffraction experiment. Experimental phasing is one technique to solve this phase problem; it usually requires the incorporation of heavy atoms in the protein crystal. Conventional derivatisation with heavy-metal salts often suffers from non-specific binding, resulting in low occupancy of the heavy-atom sites or derivatisation failing completely. In this thesis a new class of compounds was developed that combines heavy atoms for experimental phasing with functional groups for interaction with biological macromolecules. The lead structure is based on a benzene ring that provides a rigid scaffold. The ring is substituted with three functional groups and three heavy atoms, iodine or bromine, respectively . Minimize

Publisher:

Göttingen : Niedersächsische Staats- und Universitätsbibliothek

Year of Publication:

2010

Subjects:

35.6235.7635.90

35.6235.7635.90 Minimize

DDC:

540 Chemistry & allied sciences *(computed)*

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Title:

5-Amino-2,4,6-triiodoisophthalic acid monohydrate

Description:

The title compound, C8H4I3NO4·H2O, shows an extensive hydrogen-bond network; in the crystal structure, molecules are linked by OH.O, NH.O and OH.N hydrogen bonds involving all possible donors and also the water molecule.

The title compound, C8H4I3NO4·H2O, shows an extensive hydrogen-bond network; in the crystal structure, molecules are linked by OH.O, NH.O and OH.N hydrogen bonds involving all possible donors and also the water molecule. Minimize

Publisher:

International Union of Crystallography

Year of Publication:

2008-07-01T00:00:00Z

Document Type:

article

Language:

English

Subjects:

LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; DOAJ:Chemistry (General) ; DOAJ:Chemistry ; LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; DOAJ:Chemistry (General) ; DOAJ:Chemistry ; LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; DOAJ:Chemistry (General) ; DOAJ:Chemistry ; LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; LCC:Che...

LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; DOAJ:Chemistry (General) ; DOAJ:Chemistry ; LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; DOAJ:Chemistry (General) ; DOAJ:Chemistry ; LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; DOAJ:Chemistry (General) ; DOAJ:Chemistry ; LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q ; LCC:Chemistry ; LCC:QD1-999 ; LCC:Science ; LCC:Q Minimize

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http://scripts.iucr.org/cgi-bin/paper?S1600536808017741

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Title:

Formal Desingularization of Surfaces – The Jung Method Revisited

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Abstract. In this paper we propose the concept of formal desingularizations as a substitute for the resolution of algebraic varieties. Though a usual resolution of algebraic varieties provides more information on the structure of singularities there is evidence that the weaker concept is enough for many computational purposes. We give a detailed...

Abstract. In this paper we propose the concept of formal desingularizations as a substitute for the resolution of algebraic varieties. Though a usual resolution of algebraic varieties provides more information on the structure of singularities there is evidence that the weaker concept is enough for many computational purposes. We give a detailed study of the Jung method and show how it facilitates an efficient computation of formal desingularizations for projective surfaces over a field of characteristic zero, not necessarily algebraically closed. The paper includes a generalization of Duval’s Theorem on rational Puiseux parametrizations to the multivariate case and a detailed Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2012-11-21

Source:

http://arxiv.org/pdf/0801.2282v1.pdf

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Document Type:

text

Language:

en

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Metadata may be used without restrictions as long as the oai identifier remains attached to it.

Metadata may be used without restrictions as long as the oai identifier remains attached to it. Minimize

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Title:

FORMAL DESINGULARIZATION OF SURFACES – THE JUNG METHOD REVISITED –

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Abstract. In this paper we propose the concept of formal desingularizations as a substitute for the resolution of algebraic varieties. Though a usual resolution of algebraic varieties provides more information on the structure of singularities there is evidence that the weaker concept is enough for many computational purposes. We give a detailed...

Abstract. In this paper we propose the concept of formal desingularizations as a substitute for the resolution of algebraic varieties. Though a usual resolution of algebraic varieties provides more information on the structure of singularities there is evidence that the weaker concept is enough for many computational purposes. We give a detailed study of the Jung method and show how it facilitates an efficient computation of formal desingularizations for projective surfaces over a field of characteristic zero, not necessarily algebraically closed. The paper includes a generalization of Duval’s Theorem on rational Puiseux parametrizations to the multivariate case and a detailed Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2008-07-01

Source:

http://www.ricam.oeaw.ac.at/publications/reports/07/rep07-31.pdf

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text

Language:

en

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Contents

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Title:

ADJOINT COMPUTATION FOR HYPERSURFACES USING FORMAL DESINGULARIZATIONS

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Abstract. We show how to use formal desingularizations (defined earlier by the first author) in order to compute the global sections (also called adjoints) of twisted pluricanonical sheaves. These sections define maps that play an important role in the birational classification of schemes.

Abstract. We show how to use formal desingularizations (defined earlier by the first author) in order to compute the global sections (also called adjoints) of twisted pluricanonical sheaves. These sections define maps that play an important role in the birational classification of schemes. Minimize

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The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2012-01-29

Source:

http://www.ricam.oeaw.ac.at/publications/reports/08/rep08-02.pdf

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text

Language:

en

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Metadata may be used without restrictions as long as the oai identifier remains attached to it.

Metadata may be used without restrictions as long as the oai identifier remains attached to it. Minimize

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Title:

1.1 Solving Zero-Dimensional Systems. 2

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We document software written by the author during its time at RICAM. Implementations are done in MAGMA [4] and provided for download [1]. They have been improved during a stay with the MAGMA-group at Sydney University. We

We document software written by the author during its time at RICAM. Implementations are done in MAGMA [4] and provided for download [1]. They have been improved during a stay with the MAGMA-group at Sydney University. We Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2008-08-14

Source:

http://www.ricam.oeaw.ac.at/publications/reports/08/rep08-08.pdf

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text

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en

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Contents

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Abstract. We present a new method for the rational parametrization of plane algebraic curves. The algorithm exploits the shape of the Newton polygon of the defining implicit equation and is based on methods of toric geometry.

Abstract. We present a new method for the rational parametrization of plane algebraic curves. The algorithm exploits the shape of the Newton polygon of the defining implicit equation and is based on methods of toric geometry. Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2008-07-01

Source:

http://www.ricam.oeaw.ac.at/publications/reports/05/rep05-08.pdf

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text

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en

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Title:

COMPUTATIONAL FORMAL RESOLUTION OF SURFACES IN P 3 C

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In Algebraic Geometry smooth varieties are (in general) well-understood. By contrast (or simply because of that) the objects of interest are often singular varieties. From the theoretical point of view a remedy for this situation is the famous Theorem of Hironaka [8] on the resolution of singularities: If X is a variety over a field of character...

In Algebraic Geometry smooth varieties are (in general) well-understood. By contrast (or simply because of that) the objects of interest are often singular varieties. From the theoretical point of view a remedy for this situation is the famous Theorem of Hironaka [8] on the resolution of singularities: If X is a variety over a field of characteristic 0 then there always exists a smooth variety ˜ X and a proper birational morphism π: ˜ X → X. So for proving theorems and defining birational invariants, one can argue on ˜ X rather than on X and finally transfer the result back to the singular variety. This theorem has been made constructive by Villamayor [10], Bierstone-Milman [3] and others. There are also two implementations of the resolution algorithm in Singular, one by Anne Frübis-Krüger [6] and another by Gábor Bodnár and the second author [4]. In principal this makes many theoretical results algorithmic, but any algorithm relying on a resolution suffers from the high computational complexity of the resolution process. Minimize

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The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2013-11-07

Source:

http://magma.maths.usyd.edu.au/conferences/Magma2006/Abstracts/Beck.pdf

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Document Type:

text

Language:

en

DDC:

516 Geometry *(computed)*

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Title:

Approximate Roots in Graded Rings

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An approximate root of an univariate polynomial over a graded ring A is an element in A for which the evaluated polynomial vanishes up to a prescribed order. We give an algorithm for deciding existence of approximate roots and computing essentially all of them. Based on this algorithm we also suggest a finite representation for multivariate alge...

An approximate root of an univariate polynomial over a graded ring A is an element in A for which the evaluated polynomial vanishes up to a prescribed order. We give an algorithm for deciding existence of approximate roots and computing essentially all of them. Based on this algorithm we also suggest a finite representation for multivariate algebraic power series. Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2008-12-03

Source:

http://www.ricam.oeaw.ac.at/publications/reports/05/rep05-03.pdf

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text

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en

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Title:

Object-Oriented Content

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Abstract. We show how to use formal desingularizations (defined earlier by the first author) in order to compute the global sections (also called adjoints) of twisted pluricanonical sheaves.

Abstract. We show how to use formal desingularizations (defined earlier by the first author) in order to compute the global sections (also called adjoints) of twisted pluricanonical sheaves. Minimize

Contributors:

The Pennsylvania State University CiteSeerX Archives

Year of Publication:

2012-11-21

Source:

http://arxiv.org/pdf/0801.2286v1.pdf

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text

Language:

en

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