Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena

2022 ◽  
pp. 140757
Author(s):  
Bruno Rizzuti
Keyword(s):  
Molecular Simulations ◽  
Biological Phenomena ◽  
Physical Interactions

CALIBRATION AND RANKING OF COARSE-GRAINED MODELS IN MOLECULAR SIMULATIONS USING BAYESIAN FORMALISM

2017 ◽  
Vol 7 (2) ◽  
pp. 99-115 ◽  
Author(s):  
Hadi Meidani ◽  
Justin B. Hooper ◽  
Dmitry Bedrov ◽  
Robert M. Kirby
Keyword(s):  
Molecular Simulations ◽  
Coarse Grained

Historicity of Ecocriticism and Ecocritical History: An Introductory Overview

IJOHMN ◽  
2019 ◽  
Vol 5 (3) ◽  
pp. 22-52
Author(s):  
Jalal Uddin Khan
Keyword(s):  
Extended Family ◽  
Nobel Laureate ◽  
Amazon Rainforest ◽  
Sixth Grader ◽  
Leafcutter Ants ◽  
Biological Phenomena ◽  
Science Story ◽  
Introductory Overview ◽  
Popular Magazine ◽  
Living Organisms

Overlapping and interconnected, interdisciplinary and heterogeneous, amorphous and multi-layered, and deep and broad as it is, countless topics on ecoliterature make ecocriticism a comprehensive catchall term that proposes to look at a text--be it social, cultural, political, religious, or scientific--from naturalist perspectives and moves us from “the community of literature to the larger biospheric community which […] we belong to even as we are destroying it” (William Rueckert). As I was in the middle of writing and researching for this article, I was struck by a piece of nature writing by an eleven year old sixth grader born to his (South Asian and American) mixed parents, both affiliated with Johns Hopkins and already proud to belong to the extended family of a Nobel Laureate in Physics. The young boy, Rizwan Thorne-Lyman, wrote, as his science story project, an incredibly beautiful essay, “A Day in the Life of the Amazon Rainforest.” Reading about the rainforest was one of his interests, I was told. In describing the day-long activities of birds and animals among the tall trees and small plants, the 2 pp.-long narrative actually captures the eternally continuing natural cycle of the Amazon. The budding naturalist’s neat classification of the wild life into producers (leafy fruit and flowering plants and trees), consumers (caimans/crocodiles, leafcutter ants, capuchin monkey), predators (macaws, harpy eagles, jaguars, green anaconda), decomposers (worms, fungi and bacteria), parasites (phorid flies) and scavengers (millipedes) was found to be unforgettably impressive. Also the organization of the essay into the Amazon’s mutually benefitting and organically functioning flora and fauna during the day--sunrise, midday, and sunset--was unmistakably striking. I congratulated him as an aspiring environmentalist specializing in rain forest. I encouraged him that he should try to get his essay published in a popular magazine like Reader’s Digest (published did he get in no time indeed![i]) and that he should also read about (and visit) Borneo in Southeast Asia, home to other great biodiverse rainforests of the world. I called him “soft names” as a future Greenpeace and Environmental Protection leader and theorist, a soon-to-be close friend of Al Gore’s. The promising boy’s understanding, however short, of the Amazon ecology and ecosystem and the biological phenomena of its living organisms was really amazing. His essay reminded me of other famous nature writings, especially those by Fiona Macleod (see below), that are the pleasure of those interested in the ecocriticism of the literature of place--dooryards, backyards, outdoors, open fields, parks and farms, fields and pastures, and different kinds of other wildernesses.   [i] https://stonesoup.com/post/a-day-in-the-life-in-the-amazon-rainforest/

The Dialogical concept of consciousness in L.S. Vygotsky and G.H. Mead and its relevance for contemporary discussions on consciousness

2011 ◽  
Vol 42 (2) ◽  
pp. 65-70 ◽  
Author(s):  
Leszek Koczanowicz
Keyword(s):  
Activity Theory ◽  
Interpersonal Relationships ◽  
Social Relationships ◽  
Social Relations ◽  
Human Consciousness ◽  
Cultural Activity ◽  
Contemporary Philosophy ◽  
Biological Phenomena ◽  
Complex Process ◽  
The World

The Dialogical concept of consciousness in L.S. Vygotsky and G.H. Mead and its relevance for contemporary discussions on consciousness In my paper I show the relevance of cultural-activity theory for solving the puzzles of the concept of consciousness which encounter contemporary philosophy. I reconstruct the main categories of cultural-activity theory as developed by M.M. Bakhtin, L.S. Vygotsky, G.H. Mead, and J. Dewey. For the concept of consciousness the most important thing is that the phenomenon of human consciousness is consider to be an effect of intersection of language, social relations, and activity. Therefore consciousness cannot be reduced to merely sensual experience but it has to be treated as a complex process in which experience is converted into language expressions which in turn are used for establishing interpersonal relationships. Consciousness thus can be accounted for by its reference to objectivity of social relationships rather than to the world of physical or biological phenomena.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulations

2019 ◽  
Author(s):  
Riccardo Spezia ◽  
Hichem Dammak
Keyword(s):  
Degrees Of Freedom ◽  
Molecular Simulations ◽  
Zero Point ◽  
Thermal Bath ◽  
Unimolecular Dissociation ◽  
Point Energy ◽  
Rotational Degrees Of Freedom ◽  
The Difference ◽  
Nuclear Effects

<div> <div> <div> <p>In the present work we have investigated the possibility of using the Quantum Thermal Bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is aimed in introducing quantum nuclear effects with a com- putational time which is basically the same as in newtonian simulations. At this end we have considered the model fragmentation of CH4 for which an analytical function is present in the literature. Moreover, based on the same model a microcanonical algorithm which monitor zero-point energy of products, and eventually modifies tra- jectories, was recently proposed. We have thus compared classical and quantum rate constant with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study unimolecular fragmentation of much complex systems with molecular simulations. The role of QTB thermostat on rotational degrees of freedom is also analyzed and discussed. </p> </div> </div> </div>

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