Using Computational Chemistry to Understand & Discover Chemical Reactions

Daedalus ◽  
2014 ◽  
Vol 143 (4) ◽  
pp. 49-66 ◽  
Author(s):  
K. N. Houk ◽  
Peng Liu

Chemistry, the “science of matter,” is the investigation of the fabulously complex interchanges of atoms and bonds that happen constantly throughout our universe and within all living things. Computational chemistry is the computer modeling of chemistry using mathematical equations that come from physics. The field was made possible by advances in computer algorithms and computer power and continues to flourish in step with developments in those areas. Computational chemistry can be thought of as both a time-lapse video that slows down processes by a quadrillion-fold and an ultramicroscope that provides a billion-fold magnification. Computational chemists can quantitatively simulate simple chemistry, such as the chemical reactions between molecules in interstellar space. The chemistry inside a living organism is dramatically more complicated and cannot be simulated exactly, but even here computational chemistry enables understanding and leads to discovery of previously unrecognized phenomena. This essay describes how computational chemistry has evolved into a potent force for progress in chemistry in the twenty-first century.

Author(s):  
Thomas Vourc’h ◽  
Julien Léopoldès ◽  
Annick Méjean ◽  
Hassan Peerhossaini

Cyanobacteria are photosynthetic micro-organisms colonizing all aquatic and terrestrial environments. The motility of such living micro-organisms should make their diffusion distinct from typical Brownian motion. This diffusion can be investigated in terms of global behavior (Fickian or not) and in terms of displacement probabilities, which provide more detail about the motility process. Using cyanobacterium Synechocystis sp. PCC 6803 as the model micro-organism, we carry out time-lapse video microscopy to track and analyze the bacteria’s trajectories, from which we compute the mean-squared displacement (MSD) and the distribution function of displacement probabilities. We find that the motility of Synechocystis sp. PCC 6803 is intermittent: high-motility “run” phases are separated by low-motility “tumble” phases corresponding to trapped states. However, this intermittent motility leads to a Fickian diffusive behavior, as shown by the evolution of the MSD with time.


Blood ◽  
2010 ◽  
Vol 116 (6) ◽  
pp. 909-914 ◽  
Author(s):  
Enid Yi Ni Lam ◽  
Christopher J. Hall ◽  
Philip S. Crosier ◽  
Kathryn E. Crosier ◽  
Maria Vega Flores

Abstract Blood cells of an adult vertebrate are continuously generated by hematopoietic stem cells (HSCs) that originate during embryonic life within the aorta-gonad-mesonephros region. There is now compelling in vivo evidence that HSCs are generated from aortic endothelial cells and that this process is critically regulated by the transcription factor Runx1. By time-lapse microscopy of Runx1-enhanced green fluorescent protein transgenic zebrafish embryos, we were able to capture a subset of cells within the ventral endothelium of the dorsal aorta, as they acquire hemogenic properties and directly emerge as presumptive HSCs. These nascent hematopoietic cells assume a rounded morphology, transiently occupy the subaortic space, and eventually enter the circulation via the caudal vein. Cell tracing showed that these cells subsequently populated the sites of definitive hematopoiesis (thymus and kidney), consistent with an HSC identity. HSC numbers depended on activity of the transcription factor Runx1, on blood flow, and on proper development of the dorsal aorta (features in common with mammals). This study captures the earliest events of the transition of endothelial cells to a hemogenic endothelium and demonstrates that embryonic hematopoietic progenitors directly differentiate from endothelial cells within a living organism.


1994 ◽  
Vol 179 (2) ◽  
pp. 601-608 ◽  
Author(s):  
C M Alpuche-Aranda ◽  
E L Racoosin ◽  
J A Swanson ◽  
S I Miller

Light microscopic studies of phagocytosis showed that Salmonella typhimurium entered mouse macrophages enclosed in spacious phagosomes (SP). Viewed by time-lapse video microscopy, bone marrow-derived macrophages exposed to S. typhimurium displayed generalized plasma membrane ruffling and macropinocytosis. Phagosomes containing Salmonella were morphologically indistinguishable from macropinosomes. SP formation was observed after several methods of bacterial opsonization, although bacteria opsonized with specific IgG appeared initially in small phagosomes that later enlarged. In contrast to macropinosomes induced by growth factors, which shrink completely within 15 min, SP persisted in the cytoplasm, enlarging often by fusion with macropinosomes or other SP. A Salmonella strain containing a constitutive mutation in the phoP virulence regulatory locus (PhoPc) induced significantly fewer SP. Similar to Yersinia enterocolitica, PhoPc bacteria entered macrophages in close-fitting phagosomes, consistent with that expected for conventional receptor-mediated phagocytosis. These results suggest that formation of SP contributes to Salmonella survival and virulence.


Author(s):  
Mark Lorch

Biochemistry: A Very Short Introduction discusses the key concepts of biochemistry, as well as the historical figures in the field and the molecules they studied. From bacteria to humans, all living things are composed of cells of one type or another, all of which have fundamentally the same chemistry. Biochemistry is the study of the chemical reactions within these cells; the molecules that are created, manipulated, and destroyed as a result of them; and the chemical structures such as DNA on which these biochemical reactions take place. This VSI considers the current science and innovations in the field. It also looks at the interaction between biochemistry, biotechnology, and synthetic biology.


2003 ◽  
Vol 1855 (1) ◽  
pp. 97-104 ◽  
Author(s):  
Christopher Strong ◽  
Scott Lowry ◽  
Peter McCarthy

An innovative application of time-lapse video recording is used to assist in an evaluation of a highway safety improvement. The improvement is an icy-curve warning system near Fredonyer Summit in northern California that activates real-time motorist warnings via extinguishable message signs, based on weather readings collected from road weather information systems. A measure of effectiveness is whether motorist speed is reduced as a result of real-time warnings to drivers. Why indirect speed measurement with video was preferred over radar for this case is discussed, as is how specific methodological issues related to the custom-built equipment, including camera location and orientation, distance benchmarking, and data collection and reduction. Theoretical and empirical accuracy measurements show that the video surveillance trailers yield results comparable to radar and, hence, would be applicable for studies in which speed change is measured. Because this particular technology had not been used previously, several lessons are documented that may help determine where and how similar equipment may be optimally used in future studies.


1991 ◽  
Vol 22 (3) ◽  
pp. 275-276
Author(s):  
B. Nys ◽  
A. Van Daele ◽  
W. Jacob

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