Complexity Science
Project title: Affect of orientation distributions of fibres on spectroscopic data: fluid flow, light scattering and polarized light spectroscopies.
Supervisor (the person who will be doing the day to day supervision of the mini-project):
Name: Alison Rodger______
Department: Chemistry______Building, Room: B607______
E-mail address: ______Phone number: 74696/07920531213______
Project advisor: Dave Smith, Birmingham (fluid dynamics, )
Project proposal:
A.Background to project
Most biological systems operate in an aqueous phase often crowded with other molecules and molecular assemblies. Very few techniques give structural information in solution for the more complex molecular assemblies such as lipid bilayers, fibres and DNAs. Linear dichroism which is the differential absorption of two polarizations of light is ideally designed to provide data on these large molecular systems that can be flow oriented. We have recently invented a Raman analogue, Raman linear difference spectroscopy. If the method of detection is linear dichroism (LD) then the measured signal may be expressed in terms of independent orientation and spectroscopic factors:
LD =Z2 – Y2 = ½(3cos2–1) ½(3cos2–1) (1)
where and are as defined in the figure below.
The Raman equations are more complicated since Raman is a scatterign phenomenon [Kowaslka et al.].
In a 2010–2011 MOAC mini-project J. McLachlan calculated the orientation distribution of rigid rods in flow and applied that to linear dichroism spectroscopy. We are in the process of writing the paper that reports how well this agrees with experiment and enables experimental data to be further analysed. This first stage of work leaves two major issues
(i)The LD signal is dependent on particle length so when we use LD to investigate kinetics we are not measuring a property that is linearlydependent on disapperance of reactant or appearance of product.
(ii)Raman linear difference spectroscopy (RLD, which has recently been invented at Warwick [Kowalska et al.]) has a more complicated orientation distribution/optical factor equation which is a sum of a numebr of terms rather than a simple product of orientation and spectroscopic factors.
B.Programme of work
The programme of work will involve the following.
(i)Exploring theoretically and computationally the dependence of linear dichroism signal on particle length and applying this understanding to the analysis of fibre growth kinetics. Applications will focus on the cytoskeletal protein FtsZ though will commence with DNAs of known length. This will initially follow methods outlined in McLachlan et al.This will be related to scattering data which is also not linearly dependent on reactant or product concentration and complements LD.
(ii)Determine the dependence of RLD on shear rate and the effect this might have on analysis of RLD data of biomacromolecules.
C.Skills to be learned
The skills that will be acquired include applications of spectroscopy theory, including basic quantum electrodynamics, aspects of fluid dynamics and modelling of flows, understanding of biomacromolecular fibrous systems. This project is challenging as it cover a range of theoretical disciplines and will require mastery of fluid dynamics literature.
D.Outcomes, beneficiaries and follow-up
It is hoped that the end goal will be a methodology for experimentalists to analyse their experimental linear dichroism data to give kinetic and steady state parameters without needing to understand the underlying theory. It is predicated on the fact that linear dichroism and Raman linear difference spectroscopy contain significantly more information than we currently know how to extract. This is a first step in determining how to extract that information and use it to charcaterise biomolecular systems that are challenging to study by more traditional methods.
E.Outline of a literature review, including starting references.
Rittman, M., E. Gilroy, et al. (2009). "Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review." Science Progress 92: 163-204.
Takeuchi, H. M., M.; Overman, S.A.; Thomas, G.J. (1996). "Raman linear intensity difference of flow-oriented macromolecules: orientation of the indole ring of tryptophan-26 in filamentous virus fd." J. Am. Chem. Soc. 118: 3498-3507.
Kowalska,P.;Cheeseman, J.R.;Razmkah, K.; Green, B.;Nafie, L.A.;Rodger, A. “Experimental and theoretical polarized Raman linear difference spectroscopy of small molecules with a new alignment method using stretched polyethylene film” Analytical Chemistry, 2012,
McLachlan, J.; Smith, D.; Rodger, A; "Spectroscopic Detection of Flow-induced Orientation Distributions" 2012, in preparation (available on request)
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