Job description and selection criteria

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_____________________________________________
______
______________________

DEPARTMENT OF PHYSICS



I
NSERT DIVISION
LOGO
/
NAME

Job description and selection criteria


Job title

Marie Curie Early Stage Researcher

(ESR)

x 3

Division

Mathematical, Physical & Life Sciences Division

Department

Department of
Physics

Location

Clarendon Laboratory, Parks Road, Oxford

Benefits

A full employment contract. Benefits associated with Marie Curie
Fellowships including full social security,
living and
mobility
allowances.

Hours

Full time

Contract type

Fixed
-
term
(36 months)

Reporting to


Professor Andrew Turberfield

Vacancy reference

106460

Additional
information

Closing date


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2


The University


The University of Oxford is a complex and stimulating organisation, which enjoys an
international reputation as a world
-
class centre of excellence in research and teaching. It
employs over 10,000 staff and has a student population of over 21,000.


Most st
aff are directly appointed and managed by one of the University’s 130 departments or
other units within a highly devolved operational structure
-

this includes 5,900 ‘academic
-
related’ staff (postgraduate research, computing, senior library, and administra
tive staff) and
2,820 ‘support’ staff (including clerical, library, technical, and manual staff). There are also
over 1,600 academic staff (professors, readers, lecturers), whose appointments are in the
main overseen by a combination of broader divisional
and local faculty board/departmental
structures. Academics are generally all also employed by one of the 38 constituent colleges
of the University as well as by the central University itself.


Our annual income in 2009/10 was £879.8m. Oxford is one of Eur
ope's most innovative and
entrepreneurial universities: income from external research contracts exceeds £367m p.a.,
and more than 60 spin
-
off companies have been created.


For more information please visit
www.ox.ac.uk


Mathematical, Physical & Life Sciences Division


The Mathematical, Physical and Life Sciences (MPLS) Division is one of the four academic
divisions of the University of Oxford. We have over 6,000 students and research staff, and
generate over half of our f
unding from external research grants.


The MPLS Division's
10 departments and 3 interdisciplinary units

span the full spectrum of
the mathematical, computational, physical, engineering and life sciences,

and undertake
both fundamental research and cutting
-
edge applied work. Our research addresses major
societal and technological challenges and is increasingly interdisciplinary in nature. We
collaborate closely with colleagues in Oxford across the medical
sciences, social sciences
and humanities.

Today's scientific research not only crosses traditional subject boundaries, but also
transcends national boundaries: MPLS scientists collaborate with researchers from around
the world, and play leading roles in ma
ny international projects.


For more information please visit:
http://www.mpls.ox.ac.uk/home



Department of Physics


Oxford Physics is one of the largest and most eminent departments in Europe


pursuing
fore
front research alongside training the next generation of leaders in Physics.


With an academic staff of almost one hundred our activities range from fundamental
particles to the furthest reaches of the universe to manipulating matter on an atomic scale.
Oxford physicists are probing new ways to harness solar energy, modelling the Earth's
atmosphere to predict the future climate, exploring computation on the quantum scale and
executing calculations that reveal the fundamental structure of space and time.


For more information please visit:
http://www.physics.ox.ac.uk/



3



Sub
-
department
of Condensed Matter Physics


The post
-
holder will be based in the Condensed Matter sub
-
department, which is one of the
seven sub
-
d
epartments that together make up the Department of Physics; these are
Astrophysics, Atomic and Laser Physics, Atmospheric, Oceanic and Planetary Physics,
Condensed Matter Physics, Particle Physics and Theoretical Physics. Members of all sub
-
departments ta
ke part in research, teaching and matters such as examinations, discussion
of syllabi, lectures and liaison with undergraduates and postgraduate students.


Condensed Matter Physics includes a substantial Biological Physics Research Group


see
http://www2.physics.ox.ac.uk/research/biological
-
physics


Job description

Research topic

Marie Curie Integrated Training Network:

European School of DNA Nanotechnology (EScoDNA)

Principal Investigator
/ supervisor

Prof. Andrew Turberfield

Project web site

http://www.escodna.eu/

Funding partner

The funds supporting this research pro
ject are provided by the
EU

Re
search Framework programme
FP7 P
eople


Marie Curie
Actions


Overview of the role


The main purpose of these
Early Stage Researcher (
ESR
)

positions is to provide training
through research into the applications of self
-
assembled nanostructures for the control of
biological systems. T
his interdisciplinary project is part of the Marie Curie Integrated Training
Network for the advancement of re
search into DNA nanotechnology, EScoDNA. The
candidate will develop techniques for the
design,
construction and characterization of
synthetic molecular machinery and its application for the control of biological systems,
including cells, biological structu
res such as membranes and biomolecules.

Please see below for individual
research
project descriptions

N.B. These

position
s are

suitable for a student embarking on a first doctoral degree.
They
are also suitable as

first postdoctoral position
s for
research
er
s

who, at the time of
appointment, is close to completing a PhD at another university but has not yet been
awarded this degree.
An Oxford D.Phil. is a ‘deliverable’ of this training grant: in the second
case,
an ESR

would obtain a second doctoral degree
in the course of this employment.


EScoDNA ITN
(
http://escodna.eu)


DNA Nanotechnology is a new and emerging interdisciplinary area with the potential to
become a leading technological foundation for the development of future medicines,
diagnostic tools, materials, optics and electronics. The purpose of establishing a Mari
e Curie
ITN is to establish a coherent and focused program between leading scientists in the EU to
train young scientists and future leaders in this strategic interdisciplinary research area.

4


Hands
-
on research training forms an important part of
EScoDNA IT
N. It will be conducted
through research projects in the following areas:


A) design of functional

and dynamic DNA nanostructures

B) integration of other
materials in DNA nanostructures

C) application of DNA nanotechnolo
gy in life science and medicine


The integration of functions, dynamics (A) and new materials (B) forms the basis for the
application of DNA nanostructures as novel tools in key application areas in life sciences and
medicine (C)
-

for example, achieve controlled passage through cellular
membranes,
allowing reliable and cell
-
specific drug or gene delivery. In principle, DNA structures provide
all the essential properties required for this task and can be employed as information
-
processing and active agents in biological surroundings.

DNA
nanotechnology is based on the unique self
-
assembly properties of DNA and other
nucleotide derivatives which allow the rational design and formation of nanoscale structures
with predictable geometry and function [Seeman, N. C. Nature 421, 427 (2003); Bath,

J. and
Turberfield A. J. Nature Nanotechnol. 2, 275 (2007) ]. It includes studies of the basic self
-
assembly properties of nucleobases and the cooperative assembly of large assemblies of
hundreds of DNA strands. DNA self
-
assembly is controlled by the hybr
idization of DNA
strands with complementary base sequences to create the Watson
-
Crick double helix. DNA
sequences of more than 150 nucleotides can be synthesized chemically by automated
synthesis, making it possible for scientists to program their interact
ions with other synthetic
or natural DNA strands and thus to design assembly pathways.

By computer aided design, highly complex 2D and 3D DNA structures can be rapidly
designed and manufactured in a parallel self
-
assembly process using large pools of DNA
strands. The dynamic properties of DNA also allow the formation of mechanically functional
and programmable DNA devices such as DNA walkers, DNA actuators and a variety of DNA
sensors. The chemical synthesis of DNA makes it possible to insert modified base
s and non
-
natural chemical modifications at specific positions of the synthetic DNA strands. Such
modifications include fluorophores, biotin and, in particular, reactive chemical linkers that in
turn make it possible to covalently attach other molecules to

DNA. In this way, molecular
electronic components, bioactive compounds, polymers, dendrimers and mechanically
functional molecules can be incorporated into DNA nanostructures. Chemical linkers that
enable conjugation to other materials, in particular prot
eins, make it possible to integrate
nature’s complex machinery into DNA nanostructures.

EScoDNA

combines training through res
earch with a carefully designed and

strongly
interlinked programme of research projects

at eight leading European universities and
commercial partners:


Aarhus University
, Aarhus, Denmark

Ludwig
-
Maximilians
-
University
, Munich, Germany

The Technic
al University of Munich
, Munich Germany

Karolinska Institutet
, Stockholm, Sweden

University of Oxford
, Oxford, United Kingdom

Vipergen ApS
, Copenhagen, Denmark

baseclick GmbH
, Munich, Germany

Microsoft

Research
, Cambr
idge United Kingdom (Associate P
artner).


A coordinated

network
-
wide training
programme
will be provided by experts within the field
;
this will

be closely interlinked with research

programmes
.
ESRs will visit partner institutions
on secondment as an integral part of their individual training project.



5



Individual research projects


Pro
ject 1 “
Dynamic
DNA S
tructures

for Control of Biological Systems


One of the most exciting properties of DNA na
nostructures is their ability to change shape
and move in response to external stimuli. We propose to design dynamic nanostructures


molecular robots
-

that are functionalized to mediate interaction with biological molecules
and structures

and to explore
their potential to exert active control over their environments
outside and within cells. Potential stimuli for shape change include DNA and RNA and,
through incorporation of specific aptamers, proteins and small molecules such as ATP,
creating the possibi
lity of structures that respond to biologically relevant stimuli.

The project will include secondment to Ludwig Maximilians University.


P
roject 2


DNA
structures
for functional control of proteins


We will investigate the ability of DNA cages to deliver
protein cargos within cells and to

control their activity by selectively impeding or facilitating their interaction with other

large
biomolecules, potentially creating smart drug delivery vehicles.
Cages will

be functionalized
to facilitate

targeting and i
nteraction

with the membrane, and that the cage
-
opening
activation mechanism can also be

independently engineered without requiring modification
of the cargo.

The project will include secondment to
Aarhus
University.


Project 3 “
Computation by

and operatio
n of

synthetic

molecular motors

made from DNA


We
will

develop computing systems based on
DNA
automata
, capable of controlled motion,
navigating self
-
assembled
network
s

of tracks
. Applications include biomolecular

computation, molecular systems for analysis and local control of chemical synthesis
including
drug manufacture or

delivery.

The project will
be co
-
supervised by Prof. Luca Cardelli. It will
combine experimental and
theoretical investigations and will inc
lude secondment to Microsoft Research Cambridge to
work on the development of software tools for automated design and verification.


References:


DNA Cage Delivery to Mammalian Cells.

A. S. Walsh, H. F. Yin, C. M. Erben, M. J. A. Wood, A. J. Turberfield.

ACS Nano

5
,
5427
-
5432 (2011)


A DNA
-
based molecular motor that can navigate a network of tracks.

S. F. J. Wickham, J. Bath, Y. Katsuda, M. Endo, K. Hidaka, H. Sugiyama, A. J. Turberfield.

Nature Nanotechnol.
7
,

169
-
173

(2012)


Coordinated chemomechanical

cycles: a mechanism for autonomous molecular motion

S. J. Green, J. Bath, and A. J. Turberfield

Phys. Rev. Lett.
101
, 238101 (2008)


Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication

R. P. Goodman, I. A. T. Schaap , C. F Ta
rdin, C. M. Erben, R.M. Berry, C. F. Schmidt and
A.

J.

Turberfield

Science
310
, 1661
-
1665 (2005)


Design and analysis of DNA strand displacement devices using probabilistic model checking


6


M. R. Lakin, D. Parker, L. Cardelli, M. Kwiatkowska, A. Phillips

J.

Roy. Soc. Interface

9
, 1470
-
1485 (2012)


Abstractions for DNA circuit design

M. R. Lakin, S. Youssef, L. Cardelli, A. Phillips

J. Roy. Soc. Interface

9
, 470
-
468 (2012)


Key
r
esponsibilities

of
an
ESR




Participate in EScoDNA

training programme, including secondment to network
partners



D
evelop
a
Personal Career Development Plan which will address

generic, transferable
and task
-
specific skills training needs



Manage own academic research and administrative activities. This invol
ves small
scale project management, to co
-
ordinate multiple aspects of work to meet deadlines



Adapt existing and develop new scientific techniques and experimental protocols



Use specialist scientific equipment in a laboratory environment



Test hypotheses an
d analyse scientific data from a variety of sources, reviewing and
refining working hypotheses as appropriate



Contribute ideas for new research projects



Work collaboratively with colleagues on all aspects of research, including in the
preparation of scien
tific reports and journal articles and presentation of papers and
posters



Represent the research group at external meetings/seminars, either with other
members of the group or alone



Carry out collaborative projects with colleagues in partner institutions
and research
groups.



Share in communal tasks associated with the smooth running of the research group.



Provide help and advice to colleagues where appropriate.



Participate in journal club meetings


Person specification and s
e
l
ection criteria



An ESR

posi
tion is s
uitable
for a student embarking on a first doctoral degree.
It is also
suitable as a first postdoctoral position for a researcher who, at the time of
appointment, is close to completing a PhD at another university but has not yet been
awarded this

degree.

An Oxford D.Phil. is a ‘deliverable’ of this training grant: in the second
case, the candidate would obtain a second doctoral degree in the course of this
employment.

Applications are invited from recent graduates, final year undergraduates or those already
undertaking a PhD programme but fitting the eligibility criteria.


Essential



Applicants should hold or expect to gain a first or upper second class honours degree
or equivalent in a relevant discipline
, e.g. physics, chemistry, biochemistry, molecular
or cellular biology, engineering
, computer science
.


7




Applicants must satisfy the eligibility requirements for an Early Stage Researcher
under the European Commission Fr
amework 7 Early Stage Training Scheme listed
below:

Early Stage Researchers, ESRs
must

(at the time of recruitment by the host
organisation):


a) not yet have been awarded the doctorate degree and


b) be in the first 4 years (full
-
time equivalent) of
their research careers. This period is
measured from the date when they obtained the degree which would entitle them to
embark on a doctorate, irrespective of whether or not a doctorate is envisaged.


Mobility of Researchers requirement
:


Researchers can b
e of any nationality. They are required to undertake trans
-
national
mobility (i.e. move from one country to another) when taking up their appointment. At
the time of recruitment by the host organisation, researchers must not have resided
or carried out the
ir main activity (work, studies, etc) in the country of their host
organisation for more than 12 months in the 3 years immediately prior to the
reference date’.




Applicants must fulfil the requirements for admission as a graduate research student
at Oxford University:
http://www.ox.ac.uk/admissions/postgraduate_courses/
apply/application_guide.html


In the case of a researcher already studying for a PhD, applicants must have relevant
research experience in biophysics, biochemistry, molecular or cellular biology or
biological chemistry
or computer science
.



Good interper
so
nal and communications skills

and the ability to work as part of a
team.


Desirable



P
revious research experience in the
form of an experimental
master
s

programme

or
PhD research

i
n
an
associated field.



Particularly relevant experience includes
:

Projects
1 & 2

-

nanofabrication by biomolecular self
-
assembly, membrane biophysics,
biophysical characterization of cellular and biomolecular systems, cellular transport
processes and control mechanisms, synthetic biology, chemical fun
ctionalization of
nucleic
acids;

Project 3

-

automated techniques for design and verification;
nanofabrication by self
-
assembly; synthetic biology;
chemistry;
biophysical characterization of cellular and
biomolecular systems.


For information about working at Oxford, please see:
http://www.ox.ac.uk/about_the_university/jobs/research/



8



How

to apply


If you consider that you meet the selection criteria, click on the Apply Now button on the ‘Job
Details’ page and

follow the on
-
screen instructions to register as a user. You will then be
required to complete a number of screens with your application details, relating to your skills
and experience. When prompted, please provide details of
two r
eferees
.
You should ask

your referees to send references directly to
personnel@physics.ox.ac.uk

quoting
reference
106460

by the closing date
.

You will also be required to upload a CV

which
should include a statement of research interests
and
a covering letter
outlining your
qualifications for the project.




Please
use the following naming conventions for
uploaded documents
:



yourname_CV.pdf;

yourname_supporting.pdf.


All applications must be received by
midday

on the closing date
.


Should you experience any difficulties using the online application system, please email
recruitment.support@admin.ox.ac.uk



To return to the online application at any stage, please click on the following link
www.recruit.ox.ac.uk


Please note that you will be notified of the progress of your application by automatic

e
-
mails from our e
-
recruitment system. Please check your spam/junk mail regularly to
ensure that you receive all e
-
mails.