scholarly journals Computer Simulations in Service of Biology

2021 ◽  
Vol 8 ◽  
Author(s):  
Michael Levitt
Keyword(s):  
Computer Simulation ◽  
Structural Biology ◽  
Computer Simulations ◽  
Virtual World ◽  
Computer Game ◽  
Structure And Function ◽  
Important Research ◽  
Scientific World ◽  
The World ◽  
And Function

Computer simulation is an important research tool in today’s scientific world. Computers allow us to perform computations that mimic the behavior of complex (biological) systems in ways that we could not otherwise achieve. You could think of these simulations as a computer game, in which a virtual world is created that works according to certain (e.g., physical) rules. While we play the game, we learn the rules governing this virtual world and its environment, and also the way that we affect this world as players. In this article, I will explain how we use computer simulations in the world of structural biology to study the structure and function of molecules. I will also describe how I think that we could use insights from the world of biology and computer simulations to advance the society that we live in.

The Dispute Settlement System of the WTO: Structure and Function in the Perspective of the First 10 Years

2006 ◽  
Vol 5 (1) ◽  
pp. 49-75 ◽  
Author(s):  
Giorgio Sacerdoti
Keyword(s):  
Dispute Settlement ◽  
Structure And Function ◽  
International Justice ◽  
General Interest ◽  
Turn Of The Millennium ◽  
Settlement System ◽  
The World ◽  
Key Features ◽  
Dispute Settlement System ◽  
And Function

AbstractThe dispute settlement system of the World Trade Organization (the "WTO") presents a number of innovative features within the various models of international justice existing at the turn of the millennium. Ten years after its establishment, it is worthwhile to examine its key features in the light of a comparative analysis, exploring its strengths and weaknesses, and highlighting aspects of general interest and possible developments.

scholarly journals The effect of individual variation on the structure and function of interaction networks in harvester ants

2011 ◽  
Vol 8 (64) ◽  
pp. 1562-1573 ◽  
Author(s):  
Noa Pinter-Wollman ◽  
Roy Wollman ◽  
Adam Guetz ◽  
Susan Holmes ◽  
Deborah M. Gordon
Keyword(s):  
Computer Simulations ◽  
Information Flow ◽  
Individual Variation ◽  
Hot Spot ◽  
Interaction Network ◽  
Structure And Function ◽  
Skewed Distribution ◽  
Interaction Frequency ◽  
Harvester Ants ◽  
And Function

Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant's interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow.

scholarly journals Exploring Speech Act of English and Tshivenda Representatives and Directives

2021 ◽  
Vol 26 ◽  
pp. 372-382
Author(s):  
Farisani Thomas Nephawe ◽  
Matodzi Nancy Lambani
Keyword(s):  
Second Language ◽  
Speech Acts ◽  
Speech Act ◽  
Social Contexts ◽  
Structure And Function ◽  
The World ◽  
And Function

Competence in English pragmatics enhances the use of English in social contexts throughout the world. However, using English as a second language is always problematic particularly when it comes to the interpretation of speech act in English. The differences in structure and function between English and other languages such as Tshivenda are conspicuous. The current research explored Speech Act of English and Tshivenda representatives and directives among the Tshivenda-speaking people. The findings revealed that the Tshivenda-speaking people faced difficulties utilising English Speech Acts such as representatives, and directives. The research recommends frequent interaction between those proficient in English and Tshivenda-speaking people.

Unpacking Digital Material Mediation

2014 ◽  
Vol 18 (3) ◽  
pp. 154-182 ◽  
Author(s):  
Heather Wiltse ◽  
Keyword(s):  
Digital Technologies ◽  
Structure And Function ◽  
Responsive Materials ◽  
The World ◽  
Digital Material ◽  
And Function

Digital technologies mediate engagement with the world by making activities visible. The automaticity and physicality of the ways in which they do this suggest that it could be productive to view them as responsive digital materials. This paper explores the structure and function of responsive materials in order to develop a conceptualization of responsive digital materials. It then begins to unpack the complexities of digital material mediation through both drawing on and extending existing postphenomenological theory.

Native Mass Spectrometry: Recent Progress and Remaining Challenges

2022 ◽  
Vol 51 (1) ◽  
Author(s):  
Kelly R. Karch ◽  
Dalton T. Snyder ◽  
Sophie R. Harvey ◽  
Vicki H. Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Structural Biology ◽  
Recent Progress ◽  
Native Mass Spectrometry ◽  
Structure And Function ◽  
Annual Review ◽  
Publication Date ◽  
Analysis Software ◽  
And Function

Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The ribosome and its role in protein folding: looking through a magnifying glass

2017 ◽  
Vol 73 (6) ◽  
pp. 509-521 ◽  
Author(s):  
Abid Javed ◽  
John Christodoulou ◽  
Lisa D. Cabrita ◽  
Elena V. Orlova
Keyword(s):  
Protein Folding ◽  
Structural Biology ◽  
Polypeptide Chain ◽  
Structure And Function ◽  
Cellular Activity ◽  
Cryo Electron Microscopy ◽  
Nascent Chain ◽  
Exit Tunnel ◽  
Dynamics Simulations ◽  
And Function

Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements – the r-proteins and rRNA that line the tunnel – prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC). Advances in cryo-electron microscopy are enabling visualization of NCs within the exit tunnel, allowing early glimpses of the interplay between the NC and the ribosome. Once it has emerged from the exit tunnel into the cytosol, the NC (still attached to its parent ribosome) can acquire a range of conformations, which can be characterized by NMR spectroscopy. Using experimental restraints within molecular-dynamics simulations, the ensemble of NC structures can be described. In order to delineate the process of co-translational protein folding, a hybrid structural biology approach is foreseeable, potentially offering a complete atomic description of protein folding as it occurs on the ribosome.

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