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: a.rodger@warwick.ac.uk _____________
Phone number: 74696/07920531213 ______
Project advisor: Dave Smith, Birmingham (fluid dynamics, djsmith10@gmail.com)
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)
where  and  are as defined in the figure below.
(1)
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.
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(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 floworiented 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,
http://dx.doi.org/10.1021/ac202432e
McLachlan, J.; Smith, D.; Rodger, A; "Spectroscopic Detection of Flow-induced Orientation
Distributions" 2012, in preparation (available on request)
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