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Ugrad Research-suggestions?

  1. Jun 11, 2005 #1
    Ugrad Research-suggestions??

    I want to do research next summer. That is i want to work in a lab of some professor at my school, and hope i could get something published(not applying for grad schools, but for dental school, so the subject doesnt matter to me). And so far my background is weak in all the subjects... I did take ode,vector calc, abstract linear algebra, and orgchem1,2,cell bio, cell metabolism, but that's it. This junior year, i can of course take some advanced courses, once i figure out what i want...
    1) would i have better luck(at being published) if i did something pure bio, like "trying to figure out function of an ion channel", or something more theoretical, like biophysics? i did work in my freshman year in a bio lab and did not really like it, but at least i knew their methods, i dont know anything about physics though.

    2) lets say i want to do biophysics research. For example here are descriptions of some projects, that various researchers at my school are working on that i find interestng:
    -Biophysical chemistry with emphasis on measuring macromolecular interactions in living cells using single photon and two-photon variants of image correlation spectroscopy (ICS) and image cross-correlation spectroscopy (ICCS)
    Live cell measurement of macromolecular dynamics and clustering phenomena of green fluorescent protein (GFP) integrin constructs to study their role in assembly of cell adhesion structures and in receptor "cross-talk" with other signaling systems in cells.
    Development of new microscopic techniques that extend the capabilities of the ICS and ICCS methods. Development of a combined ICS, ICCS and imaging fluorescence resonance energy transfer microscopy. Applications of nonlinear harmonic microscopy and ICS to measurements of macromolecular mobilities in live cell systems. Application of bio-conjugated quantum dot labels for dynamic ICS measurements in living cells.
    Extension of ICS and ICCS for application to research problems in areas of neuroscience

    -We will be using the AFM for the Life Sciences facility to form a spatially controllable electrical contact to rat neurons. This will enhance our understanding of the signaling pathways in neurons, and at the same time allow us to investigate issues in interfacing semiconductors (the AFM tip) to the organic world (the neuron). We will attach a suitable signaling protein to a gold coated AFM tip (collaboration with the Lennox group). We can test the functionality of these tips by coating Au particles (=model tips) and exposing a functioning neuron to them. If it fires, the coating procedure is functional. We will then probe individual channel receptors located on a neuron by scanning the lateral position of the functionalized AFM tip. The tip-induced opening and closing of individual channels can be identified by simultaneously measuring the conductance through individual channels by patch clamp techniques commonly used in physiology

    Now i wonder what courses i would need to take in order to work in their labs? That is in order to do something useful myself? Would i need to have taken quantum mechanics1&2? And would qm be sufficient in order to do research in that? I know that 1 of those profs teaches optics in the physics dept while the other one teaches some courses "advanced materials" and "nanoscience& technology", those courses dont sound very technical(it seems like they just compliment the core physics major courses like e&m and qm)... and also optics is scheduled in the winter term to be at the same time as the quantum mechanics course.

    I also dont know whether i could handle serious courses like quantum mechanics. And in case i do well in those physics courses and start doing research in that lab, i wonder whether it will get to be only more challenging, as opposed to more interesting?? at least in bio lab, everything was simple..
  2. jcsd
  3. Jun 11, 2005 #2
    when you say weak are you speaking interms of knowledge or grades...as for publishing as a undergrad not in your senior year good luck...

    if you really wanted to do a theoretical look into mathematical biology. I do believe biophysics people have labwork. Look at your library for a book i math bio by i think her name is lisa edelstein-keshet

    topics include molecular motion, growth, population models, neuronal models, pattersn in organic formation, predator prey.
  4. Jun 11, 2005 #3
    yes, i mean weak in knowledge, i havent taken any upper level courses yet. and yes i do struggle with grades and gpa is very important, but i suck at everything. actually i took a course "math bio"-which described what you just said, and it wasnt interesting at all, it's like "chemistry of perfume"...
    i dont know anything about research. but i thought about doing research next summer and continuing into next fall, thats why i want to do it on campus. i thought that publishing was the incentive for doing this. if thats tough to do in biophysics, maybe its easier in neurobiology?

    both of the physicists that i looked up, had labs. but the problem is whether one needs to have very advanced knowledge in order to be useful in the lab and understand their experiments? in biology that is certainly not the case, general bio is enough...
  5. Jun 12, 2005 #4
    Also, by more theoretical i think i'd be more interested in something like this:
    I am investigating the phase behaviour of pure lipid bilayers, lipid bilayers with more than one lipid species, and lipid bilayers containing inclusions such as cholesterol, proteins and drug molecules. This work involves the development of Monte Carlo algorithms that are tested and applied to the above problems. One particular expertise involves the characterisation of phase behaviour using finite size scaling methods such as the Lee-Kosterlitz method to analyze the anture of the phase behaviour. New efforts are the development of a new off-lattice model for the lipid related projects, and a study of glassy behaviour in molecular crystals. of glassy behaviour in molecular crystals.
    This research aims at improving current computational methods that predict the three dimensional structure of proteins and of protein-protein interactions from the knowledge of their aminoacid sequence. Protein function is more closely related to structure than to sequence, and hence methodologies that can produce large scale predictions of protein structure are essential in this post-genomic era. Reduced, lattice based models of proteins, and Monte Carlo simulation methods are used to analyze the relationship between sequence and characteristic structural motifs of the folded protein. Statistical methods are being develop to increase sensitivity in the detection of functional sites and to calculate the thermodynamics parameters that describe protein-protein interactions (formation of dimers, trimers, etc.). The image shows the dimer of GCN4, currently being studied by replica Monte Carlo.

    now i wonder if i could contribute anything to such theoretical reserach(that is to get published)? although i'll be taking probability this fall, it does not involve any of that "monte carlo". we only learn that in the senior year, in the 2nd semester of a graduate probability course. and i dont know what are lattices(i.e. what courses people take that discuss them-group theory or graph theory?)

    also i noticed there is a far greater # of neuroscience researchers at my school, than there are physics researchers that do anything related to bio/medicine.
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