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Nonlinear two-dimensional infrared spectroscopy[39][40] is the infrared version of correlation spectroscopy. Nonlinear two-dimensional infrared spectroscopy is a technique that has become available with the development of femtosecond infrared laser pulses. In this experiment, first a set of pump pulses is applied to the sample. This is followed by a waiting time during which the system is allowed to relax. The typical waiting time lasts from zero to several picoseconds, and the duration can be controlled with a resolution of tens of femtoseconds. A probe pulse is then applied, resulting in the emission of a signal from the sample. The nonlinear two-dimensional infrared spectrum is a two-dimensional correlation plot of the frequency ω1 that was excited by the initial pump pulses and the frequency ω3 excited by the probe pulse after the waiting time. This allows the observation of coupling between different vibrational modes; because of its extremely fine time resolution, it can be used to monitor molecular dynamics on a picosecond timescale. It is still a largely unexplored technique and is becoming increasingly popular for fundamental research.

Middle Mode - Molecular (Original)

Realizing nonlinear interactions between spatially separated particles can advance molecular science and technology, including remote catalysis of chemical reactions, ultrafast processing of information in infrared (IR) photonic circuitry, and advanced platforms for quantum simulations with increased complexity. Here, we achieved nonlinear interactions at ultrafast time scale between polaritons contained in spatially adjacent cavities in the mid-IR regime, altering polaritons in one cavity by pumping polaritons in an adjacent one. This was done by strong coupling molecular vibrational modes with photon modes, a process that combines characteristics of both photon delocalization and molecular nonlinearity. The dual photon/molecule character of polaritons enables delocalized nonlinearity-a property that neither molecular nor cavity mode would have alone.

Volvox is a very interesting oogamous organism that exhibits various types of sexuality and/or sexual spheroids depending upon species or strains. However, molecular bases of such sexual reproduction characteristics have not been studied in this genus. In the model species V. carteri, an ortholog of the minus mating type-determining or minus dominance gene (MID) of isogamous Chlamydomonas reinhardtii is male-specific and determines the sperm formation. Male and female genders are genetically determined (heterothallism) in V. carteri, whereas in several other species of Volvox both male and female gametes (sperm and eggs) are formed within the same clonal culture (homothallism). To resolve the molecular basis of the evolution of Volvox species with monoecious spheroids, we here describe a MID ortholog in the homothallic species V. africanus that produces both monoecious and male spheroids within a single clonal culture. Comparison of synonymous and nonsynonymous nucleotide substitutions in MID genes between V. africanus and heterothallic volvocacean species suggests that the MID gene of V. africanus evolved under the same degree of functional constraint as those of the heterothallic species. Based on semi quantitative reverse transcription polymerase chain reaction analyses using the asexual, male and monoecious spheroids isolated from a sexually induced V. africanus culture, the MID mRNA level was significantly upregulated in the male spheroids, but suppressed in the monoecious spheroids. These results suggest that the monoecious spheroid-specific down regulation of gene expression of the MID homolog correlates with the formation of both eggs and sperm in the same spheroid in V. africanus.

A molecular evolutionary analysis of nonsynonymous and synonymous substitutions was performed between the MID ortholog of G. pectorale and those of seven other Volvocales by MEGA 6.0, using a modified Nei-Gojobori model [23,24] (assumed transition/transversion bias = 1.55).

Coot is a molecular graphics application. Its primary focus iscrystallographic macromolecular model-building and manipulation ratherthan representation i.e. more like Frodo than Rasmol.Having said that, Coot can work with small molecule (SHELXL) and electronmicroscopy data, be used for homology modelling, make passably prettypictures and display NMR structures.

Sometimes molecular replacement solutions (for example) create modelswith chains non-optimally placed relative to each other - asymmetry-related copy would be more apealling (but would be equivalent,crystalographically). For example, to move the B chain to asymmetry-related position:

The work of Meselson and Stahl in the 1950s helped us to understand that DNA replication occurs by a semi-conservative model, but it doesn't explain all of the intricate molecular movements that are necessary in order to achieve such a complicated feat. Remember that many scientists didn't agree with the semi-conservative model at first. In fact, they didn't agree with Watson and Crick's DNA model altogether because it was so elaborate. They argued that even if a molecule like this did exist in our bodies, there'd be no way for it to make copies of itself. Once they discovered the truth about the semi-conservative model, they had even more tough questions to answer. The biggest question they had was: how could a twisted, convoluted molecule like DNA open itself up for semi-conservative replication?

Remember that the semi-conservative model states that one parental strand of DNA is conserved in each of the new daughter DNA molecules. The parental strand, which is the original DNA strand, acts as a template for the daughter strand, or a strand of newly synthesized nucleotides. In order for that to happen, DNA must actually split down the middle so that all of the nitrogenous bases are exposed. Once the bases are left out in the open, then new nucleotides can be added on. Remember that there is a rule about which nucleotides pair with which; we call it the rule of complementary base pairing. So the bases adenine and thymine will always pair together, and cytosine and guanine will always pair together. That means that as the new nucleotides are being added on to form the daughter strand, they can only add on at the places where they match a complementary base. So still the question remains: how do we actually get in there to the center of the DNA double helix, unwind all the twisted strands and expose those nucleotides in the first place?

Students will do an activity in which heat is transferred from hot water to metal washers and then from hot metal washers to water. Students will view a molecular animation to better understand the process of conduction at the molecular level. Students will also draw their own model of the process of conduction.

Co-author Joonhee Lee, CaSTL research scientist, added: "To date, molecular vibrations have been pictorially explained using wiggling balls and connecting springs to represent atoms and bonds, respectively. Now we can directly visualize how individual atoms vibrate within a molecule. The images we provide will appear in textbooks to help students better understand the concept of vibrational normal modes, which till now had been a theoretical concept."

Covalent bonds are formed when electronsare shared between atoms. Hydrogen, for example, can share one pairof electrons with another atom, so we say that it forms one bond.Similarly, oxygen forms two, nitrogen usually forms three, and carbonforms four. (Remember the "HONC" rule...H=1, O=2, N=3, C=4, but note that unstable molecules can form, creating exceptions.) The ratiosof atoms in various molecules are expressed by their chemicalformulas. For example, "H2O" represents water, and"C6H12O6" represents glucose. However, this is only part of the story. In biology, the shape ofa molcule is often just as important as its chemical formula. Enzymes, for example, need a precise 3-dimensionalfit to their substrates, just like a baseball and a well-wornoutfielder's glove. In this investigation we will attempt to construct molecular models of some common substances from biology. In several cases, unusual properties will emerge that couldn't have been predicted from the flat projections that are usually drawn on paper. 041b061a72


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