Identification of bioprivileged molecules: expansion of a computational approach to broader molecular space

2021 ◽  
Author(s):  
Lauren M. Lopez ◽  
Brent H. Shanks ◽  
Linda J. Broadbelt
Keyword(s):  
Computational Approach ◽  
Computational Tools ◽  
Biobased Chemicals ◽  
Experimental Approaches

As interest in biobased chemicals grows, and their application space expands, computational tools to navigate molecule space as a complement to experimental approaches are imperative.

scholarly journals Predicting Immunogenicity Risk in Biopharmaceuticals

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 388
Author(s):  
Nikolet Doneva ◽  
Irini Doytchinova ◽  
Ivan Dimitrov
Keyword(s):  
Machine Learning Algorithms ◽  
Computational Tools ◽  
Binding Motifs ◽  
B Cell Epitopes ◽  
Crucial Step ◽  
Histocompatibility Complex ◽  
Alignment Algorithms ◽  
Experimental Approaches ◽  
Dynamics Simulations ◽  
Allergenicity Prediction

The assessment of immunogenicity of biopharmaceuticals is a crucial step in the process of their development. Immunogenicity is related to the activation of adaptive immunity. The complexity of the immune system manifests through numerous different mechanisms, which allows the use of different approaches for predicting the immunogenicity of biopharmaceuticals. The direct experimental approaches are sometimes expensive and time consuming, or their results need to be confirmed. In this case, computational methods for immunogenicity prediction appear as an appropriate complement in the process of drug design. In this review, we analyze the use of various In silico methods and approaches for immunogenicity prediction of biomolecules: sequence alignment algorithms, predicting subcellular localization, searching for major histocompatibility complex (MHC) binding motifs, predicting T and B cell epitopes based on machine learning algorithms, molecular docking, and molecular dynamics simulations. Computational tools for antigenicity and allergenicity prediction also are considered.

scholarly journals Processors and Processes: Exploring Computational Design and Landscape Architecture

2021 ◽  
Author(s):  
◽  
Philip Belesky
Keyword(s):  
Design Process ◽  
Landscape Architecture ◽  
Computational Design ◽  
Ecological Systems ◽  
Computational Approach ◽  
Computational Techniques ◽  
Concept Design ◽  
Computational Tools ◽  
Industrial Landscape ◽  
Post Industrial

<p>The computer can be a highly efficient drafting table. It can also be much more. Architects can use programming to engage with the computer on its own terms, and in doing so gain a better understanding of complex geometric, structural, or conceptual design scenarios. This ‘computational approach’ to design is increasingly common in architecture, but comparatively rare within landscape architecture. In this thesis I examine how and why landscape architects might employ computational design.  I start by reviewing the work of computational architects and landscape urbanists. I identify that both emphasize diagrammatic and processual strategies as a means to confront complexity and indeterminism within the design process. However, this conceptual overlap masks a technological divergence, as computational tools are presently ill-suited to the needs of landscape architects. Their focus should be shifted away from formal exploration and towards the analysis, simulation, and generation of landscape systems. Doing so would offer landscape architects new forms of representation that would overcome some of the current limitations within their design process.  To test this proposition, I create a series of generative tools, or ‘patterns’, that use computational techniques to model ecological systems. This pattern-based approach introduces a methodology that improves the accessibility and flexibility of computational design. These patterns are applied in tandem with standard computational techniques to create a concept design for a post-industrial landscape. Through this research I identify computation as a powerful tool for designing landscapes. The conceptual and technical methodologies it offers enable landscape architects to better understand and explore open-ended and indeterminate systems. Computation offers a novel opportunity to combine conceptual openness and technical rigour when designing complex landscapes.</p>

Computing Religion: A New Tool in the Multilevel Analysis of Religion

2012 ◽  
Vol 24 (3) ◽  
pp. 267-290 ◽  
Author(s):  
Kristoffer L. Nielbo ◽  
Donald M. Braxton ◽  
Afzal Upal
Keyword(s):  
Multilevel Analysis ◽  
Computational Approach ◽  
Theoretical Construct ◽  
Computational Tools ◽  
Collaborative Project ◽  
Multilevel Research ◽  
Invaluable Tool

AbstractThe computational approach has become an invaluable tool in many fields that are directly relevant to research in religious phenomena. Yet the use of computational tools is almost absent in the study of religion. Given that religion is a cluster of interrelated phenomena and that research concerning these phenomena should strive for multilevel analysis, this article argues that the computational approach offers new methodological and theoretical opportunities to the study of religion. We argue that the computational approach offers 1.) An intermediary step between any theoretical construct and its targeted empirical space and 2.) a new kind of data which allows the researcher to observe abstract constructs, estimate likely outcomes, and optimize empirical designs. Because sophisticated multilevel research is a collaborative project we also seek to introduce to scholars of religion some general computational issues, and finally applications that model behavior in religious contexts.

A Computational Approach to Conceptual Design

2002 ◽  
Author(s):  
Zeke Strawbridge ◽  
Daniel A. McAdams ◽  
Robert B. Stone
Keyword(s):  
Conceptual Design ◽  
Morphological Analysis ◽  
Design Research ◽  
Computational Approach ◽  
Design Tool ◽  
Design Stage ◽  
Concept Selection ◽  
Computational Tools ◽  
Detail Design ◽  
Conceptual Design Phase

Design research has generated many computational tools to aid the designer over the years. Most of these tools are focused on either the preliminary steps of customer need gathering or the concluding steps of embodiment or detail design. The conceptual design phase has seen fewer computational tools even though well known methods are available such as brainstorming, intrinsic and extrinsic searches and morphological analysis. In this paper a generalized computational conceptual design tool is presented to aid designers at the conceptual design stage. It relies on storing and reusing existing design knowledge to create new concept variants. Concept variants are computed using matrix manipulations, essentially creating a mathematical morphological matrix. The concept generator produces quick concepts that can be used for concept selection or as a basis for generating additional concept variants through non-computational, creative techniques.

scholarly journals A combined RNA-Seq and comparative genomics approach identifies 1,085 candidate structured RNAs expressed in human microbiomes

2020 ◽  
Author(s):  
Brayon J. Fremin ◽  
Ami S. Bhatt
Keyword(s):  
Comparative Genomics ◽  
Experimental Approach ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Computational Approach ◽  
Rna Seq ◽  
Rna Structures ◽  
Experimental Approaches

AbstractStructured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches by searching for motif structures in genomic sequence data. However, only a subset of these candidate structured RNAs, those from culturable, well-studied microbes, have been shown to be transcribed. As the human microbiome contains thousands of species and strains of microbes, we sought to apply both informatic and experimental approaches to these organisms to identify novel transcribed structured RNAs. We combine an experimental approach, RNA-Seq, with an informatic approach, comparative genomics across the human microbiome project, to discover 1,085 candidate, conserved structured RNAs that are actively transcribed in human fecal microbiomes. These predictions include novel tracrRNAs that associate with Cas9 and RNA structures encoded in overlapping regions of the genome that are in opposing orientations. In summary, this combined experimental and computational approach enables the discovery of thousands of novel candidate structured RNAs.

scholarly journals Processors and Processes: Exploring Computational Design and Landscape Architecture

2021 ◽  
Author(s):  
◽  
Philip Belesky
Keyword(s):  
Design Process ◽  
Landscape Architecture ◽  
Computational Design ◽  
Ecological Systems ◽  
Computational Approach ◽  
Computational Techniques ◽  
Concept Design ◽  
Computational Tools ◽  
Industrial Landscape ◽  
Post Industrial

<p>The computer can be a highly efficient drafting table. It can also be much more. Architects can use programming to engage with the computer on its own terms, and in doing so gain a better understanding of complex geometric, structural, or conceptual design scenarios. This ‘computational approach’ to design is increasingly common in architecture, but comparatively rare within landscape architecture. In this thesis I examine how and why landscape architects might employ computational design.  I start by reviewing the work of computational architects and landscape urbanists. I identify that both emphasize diagrammatic and processual strategies as a means to confront complexity and indeterminism within the design process. However, this conceptual overlap masks a technological divergence, as computational tools are presently ill-suited to the needs of landscape architects. Their focus should be shifted away from formal exploration and towards the analysis, simulation, and generation of landscape systems. Doing so would offer landscape architects new forms of representation that would overcome some of the current limitations within their design process.  To test this proposition, I create a series of generative tools, or ‘patterns’, that use computational techniques to model ecological systems. This pattern-based approach introduces a methodology that improves the accessibility and flexibility of computational design. These patterns are applied in tandem with standard computational techniques to create a concept design for a post-industrial landscape. Through this research I identify computation as a powerful tool for designing landscapes. The conceptual and technical methodologies it offers enable landscape architects to better understand and explore open-ended and indeterminate systems. Computation offers a novel opportunity to combine conceptual openness and technical rigour when designing complex landscapes.</p>

scholarly journals Fluid Flow Through Serieal Parallel Circular Cylinder Arranged In Tandem

2021 ◽  
Vol 4 (1) ◽  
pp. 51-56
Author(s):  
Nur Ikhsani ◽  
Nasaruddin Salam ◽  
Luther Sule
Keyword(s):  
Fluid Flow ◽  
Drag Coefficient ◽  
Experimental Testing ◽  
Computational Approach ◽  
Circular Cylinders ◽  
Distance Ratio ◽  
Pressure Contour ◽  
Parallel Circular Cylinder ◽  
Experimental Approaches ◽  
Flow Through

The Fluid flow through circular cylinders in serieal parallel positions arranged in tandem were analyzed computationally and experimentally at nine levels of Reynolds number, ReD  34,229; 47,921; 61,612; 75,304; 88,996; 102,688; 116,379; 130.071 and 143,763 The variation in the ratio of the distance between the front and rear cylinders is determined as M / D = 0.3, M / D = 0.5, M / D = 0.7,   M / D = 0.9, and M / D = 1.1. While the distance between cylinder number 2 and 3 we set constantly and determined as N / D = 5 cm. The results displayed are flow velocity with computational approach validated by flow visualization, computational pressure contour, and drag coefficient through experimental testing. The results showed that the smallest boundary layer thickness was obtained in the model with a distance ratio of M / D = 2.5, using both computational and experimental approaches. The characteristics of the minimum pressure contour and the lowest drag coefficient (CD) = 0.7572 were also obtained at the ratio of the distance M / D = 0.25 and at upstream speed of 21 m / s  

Application of Modified Bloch Waves to Image Analysis of Extended Linear Defects

1974 ◽  
Vol 32 ◽  
pp. 402-403
Author(s):  
S. Nakahara ◽  
D. M. Maher
Keyword(s):  
Image Analysis ◽  
Computational Approach ◽  
Dislocation Loops ◽  
Plane Wave Expansion ◽  
Dynamical Equations ◽  
Bloch Waves ◽  
Linear Defects ◽  
Imperfect Crystal ◽  
Localized Defects ◽  
Defective Crystals

Since Head first demonstrated the advantages of computer displayed theoretical intensities from defective crystals, computer display techniques have become important in image analysis. However the computational methods employed resort largely to numerical integration of the dynamical equations of electron diffraction. As a consequence, the interpretation of the results in terms of the defect displacement field and diffracting variables is difficult to follow in detail. In contrast to this type of computational approach which is based on a plane-wave expansion of the excited waves within the crystal (i.e. Darwin representation ), Wilkens assumed scattering of modified Bloch waves by an imperfect crystal. For localized defects, the wave amplitudes can be described analytically and this formulation has been used successfully to predict the black-white symmetry of images arising from small dislocation loops.

Learned Placebo Effects in the Immune System

2014 ◽  
Vol 222 (3) ◽  
pp. 148-153 ◽  
Author(s):  
Sabine Vits ◽  
Manfred Schedlowski
Keyword(s):  
Nervous System ◽  
Immune System ◽  
Associative Learning ◽  
Placebo Response ◽  
Immunosuppressive Drug ◽  
Immune Functions ◽  
Placebo Effects ◽  
New Therapeutic Approaches ◽  
Biological Variables ◽  
Experimental Approaches

Associative learning processes are one of the major neuropsychological mechanisms steering the placebo response in different physiological systems and end organ functions. Learned placebo effects on immune functions are based on the bidirectional communication between the central nervous system (CNS) and the peripheral immune system. Based on this “hardware,” experimental evidence in animals and humans showed that humoral and cellular immune functions can be affected by behavioral conditioning processes. We will first highlight and summarize data documenting the variety of experimental approaches conditioning protocols employed, affecting different immunological functions by associative learning. Taking a well-established paradigm employing a conditioned taste aversion model in rats with the immunosuppressive drug cyclosporine A (CsA) as an unconditioned stimulus (US) as an example, we will then summarize the efferent and afferent communication pathways as well as central processes activated during a learned immunosuppression. In addition, the potential clinical relevance of learned placebo effects on the outcome of immune-related diseases has been demonstrated in a number of different clinical conditions in rodents. More importantly, the learned immunosuppression is not restricted to experimental animals but can be also induced in humans. These data so far show that (i) behavioral conditioned immunosuppression is not limited to a single event but can be reproduced over time, (ii) immunosuppression cannot be induced by mere expectation, (iii) psychological and biological variables can be identified as predictors for this learned immunosuppression. Together with experimental approaches employing a placebo-controlled dose reduction these data provide a basis for new therapeutic approaches to the treatment of diseases where a suppression of immune functions is required via modulation of nervous system-immune system communication by learned placebo effects.

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