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Related Concept Videos

Archival Research01:40

Archival Research

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Some researchers gain access to large amounts of data without interacting with a single research participant. Instead, they use existing records to answer various research questions. This type of research approach is known as archival research. Archival research relies on looking at past records or data sets to look for interesting patterns or relationships. For example, a researcher might access the academic records of all individuals who enrolled in college within the past ten years and...
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Growth Models with Integration: Problem Solving01:27

Growth Models with Integration: Problem Solving

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In population modeling, integration provides a systematic way to determine accumulated quantities from known rates of change. One such application arises in ecology, where the total weight of a fish population in a body of water is referred to as its biomass. When the rate of growth of this biomass is known as a function of time, calculus can be used to determine the total biomass at a future date.Growth Rate and Biomass FunctionLet the growth rate of the fish population be represented by a...
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Integration by Parts: Indefinite Integrals01:26

Integration by Parts: Indefinite Integrals

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Integration by parts is a fundamental technique in calculus for evaluating integrals involving the product of two functions. It is particularly useful when direct integration is not feasible. The method is based on the product rule for differentiation, which states that the derivative of a product equals the derivative of the first function times the second, plus the first function times the derivative of the second. By integrating this identity and rearranging terms, the integration by parts...
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Integration by Parts: Definite Integrals01:23

Integration by Parts: Definite Integrals

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Definite integrals involving the product of two functions over a fixed interval can be evaluated using integration by parts. This method rewrites the integral as the difference of a product evaluated at the endpoints and a remaining definite integral that is often simpler to compute.A representative example is the definite integral of the inverse tangent function. Since there is no direct integration formula for arctan ⁡x, the integrand is rewritten as a product of arctan⁡ x and the...
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Structure of Benzene: Kekulé Model01:07

Structure of Benzene: Kekulé Model

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In 1865, August Kekule suggested the structure of benzene according to the structural theory of organic chemistry based on the three assertions—formula of benzene is C6H6, all the hydrogens of benzene are equivalent, and each carbon must have four bonds due to its tetravalency.
He proposed that benzene has a cyclic structure of six carbon atoms attached to one hydrogen atom each, with three alternating pi bonds.
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Structure of Benzene: Molecular Orbital Model01:18

Structure of Benzene: Molecular Orbital Model

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According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).
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A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery
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Archiving of Integrative Structural Models.

Helen M Berman1, Jill Trewhella2,3, Brinda Vallat4

  • 1RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA. berman@rcsb.rutgers.edu.

Advances in Experimental Medicine and Biology
|January 9, 2019
PubMed
Summary
This summary is machine-generated.

Archiving integrative/hybrid structural biology models requires new approaches. This involves federated data networks, common standards, and interoperation mechanisms for complex macromolecular assemblies.

Keywords:
Data exchangeData standardsIntegrative/hybrid modeling methodsPDBx/mmCIFProtein Data BankStructural biology federation

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Integrative/hybrid structural biology determines macromolecular structures using diverse experimental and computational methods.
  • Existing data archiving systems are inadequate for the complex requirements of integrative/hybrid modeling results.

Purpose of the Study:

  • To address the challenges in archiving integrative/hybrid structural models.
  • To propose a framework for effective data archiving in structural biology.

Main Methods:

  • Developing a federated network of archives for structural models and experimental data.
  • Establishing common data standards for integrative/hybrid modeling.
  • Creating mechanisms for data exchange and interoperation among repositories.

Main Results:

  • The proposed framework facilitates the archiving of complex structural biology data.
  • Standardization and federation enhance data accessibility and usability.
  • Interoperable systems improve data sharing and collaboration.

Conclusions:

  • A federated approach with common standards is essential for archiving integrative/hybrid structural models.
  • These advancements are crucial for the future of structural biology research.
  • Implementing these concepts will improve data management and scientific discovery.