AUSTRALIAN RESEARCH COUNCIL
DISCOVERY PROJECTS
APPLICATION FORM FOR FUNDING COMMENCING IN 2007	DP	

PROJECT ID:  DP0773445

Total number of sheets contained in this application		

Information on this form is collected in order to make recommendations to the Minister on the allocation of financial assistance under the Australian Research Council Act 200I and for post award reporting. The information collected may be passed to third parties for assessment purposes.  It may also be passed to the National Health and Medical Research Council, the National Occupational Health and Safety Commission, the Department of Foreign Affairs and Trade, the Department of Industry, Tourism and Resources, the Department of the Environment and Heritage, the Department of Education, Science and Training, the Department of Agriculture, Fisheries and Forestry and the Department of Veterans’ Affairs for the purpose of checking eligibility.  In other instances, information contained in this Proposal can be disclosed without your consent where authorised or required by law.

PART A—ADMINISTRATIVE SUMMARY

A1	ORGANISATION TO ADMINISTER FUNDING
The University of Queensland

A2	PROPOSAL TITLE
Simulating  viral evolution and genetic complexity 

A3	PARTICIPANT SUMMARY
Chief Investigators (CI), Partner Investigators (PI) and ARC Fellows (APD, ARF/QEII or APF).  Participant details are provided in Part B.
Person
number	Family name	Initials	Organisation	Role	ECR	
1	Drummond	PD	The University of Queensland	CI	  	

A4	REQUESTED SUPPORT
A4.1	Component(s) sought
Tick each relevant box.	Number sought	
 X 	Research Costs (personnel and project costs other than Fellowship salaries)		
	Australian Postdoctoral Fellowship (APD)	0	
	Australian Research Fellowship/Queen Elizabeth II Fellowship (ARF/QEII)	0	
	Australian Professorial Fellowship (APF)	0	

A4.2	Years for which support is being sought

	Year 1	X	Year 2	X	Year 3	X	Year 4		Year 5	

A5	SUMMARY DESCRIPTIONS

A5.1 		Summary of Proposal
A plain language summary of the aims, significance and expected outcomes (approx. 100 words).
Accurate computer models of living organisms represent one of the frontiers of science. This project aims to apply novel techniques developed in the field of physics to solve currently intractable problems related to modeling the evolution of complex genetic systems. We will focus on models of the genetic evolution of large virus populations. The research treats fundamental problems in theoretical biology, with relevance to many areas of evolution. We plan to leverage off recently developed computational physics techniques that automatically generate efficient computer software. This will allow rapid development and deployment of novel and accurate computer models of virus evolution.

	

A5.2 		Summary of National/Community Benefit (for publicity purposes)
A plain language summary of the national/community benefits expected to arise from this research (approx. 100 words).
This project has direct relevance to understanding the growth of viral infections, and therefore has possible practical applications in disease research and control. Examples of these are emerging diseases in humans such as those caused by HIV-1, SARS coronavirus and Dengue virus, which cause considerable human suffering throughout the world. A major part of current research into these diseases involves attempts to model the evolutionary genetics and dynamics of virus populations in order to understand how to control epidemics, develop vaccines and design drugs. The research program is designed to provide new computational modelling tools for this purpose, which may have wider applications as well.

	

A6	CLASSIFICATIONS AND OTHER STATISTICAL INFORMATION 
A6.1	National Research Priorities
National Research Priority		Priority Goal(s)	
Frontier Technologies for Building and Transforming Australian Industries		Breakthrough science, Frontier technologies, Smart information use	

A6.2	Keywords
Stochastic 		Computational	
Evolution		HIV	
Genetics		Virus	

A6.3	Research classifications (listed from highest % to lowest %)
Research Fields, Courses and Disciplines (RFCD)	%		Socio-Economic Objective
(SEO)	%	
230202	50		700101	40	
270203	30		730101	30	
280406	20		740301	30	

A6.4	Country/ies of international collaboration
NZ			

A7	ADDITIONAL DETAILS
A7.1	Have you submitted a similar Proposal to any other agency?	Yes      No  X
A7.2	Have you been granted an eligibility ruling regarding whether the Proposal falls within the area of clinical medical and/or dental research and training?
		Yes      No  X
A7.3 		Does the Administering Organisation have arrangements to manage intellectual property and facilitate commercialisation of research? 								            Yes  X    No  

If Yes, in no more than 750 characters (approx 100 words) of plain language, summarise these arrangements.
The Administering Organisation (AO) adheres to an intellectual 
property policy, approved by its governing body, which has as one of 
its aims the maximisation of benefits arising from research. The AO 
complies with the National Principles of Intellectual Property 
Management for Publicly Funded Research as amended from time to 
time. Further, the AO actively and successfully identifies, protects 
and commercialises AO technology and expertise through its corporate 
subsidiaries UniQuest Pty Ltd, IMBcom Pty Ltd (the commercialisation 
company for the Institute for Molecular Bioscience) and JKTech Pty 
Ltd (the commercialisation company for the Julius Kruttschnitt 
Mineral Research Centre).

A8	RESEARCH STUDENTS

The ARC is interested in reporting the number of Research Students that would be involved in this Proposal if it is funded.  The number of student places (full-time equivalent) that will be filled as a result of this project:

Number of Research Student Places (FTE) -	PhD	1.0	
	Masters		
	Honours	1.0	

A9	CERTIFICATION 

The Administering Organisation must obtain the required signature(s) before submitting this Proposal to the ARC.

Certification by the Deputy/Pro Vice-Chancellor (Research) or their delegate or equivalent in the Administering Organisation
I certify that—
•	I have obtained the written agreement of all participants to submit this Proposal.
•	The Head of Department has approved this Proposal.
•	This organisation supports this Proposal and if successful will provide basic infrastructure and the items listed in the budget for the project.
•	I have obtained the written agreement of other organisations involved in this Proposal to provide the agreed support.
•	Approval of the Partner Investigator’s participation to the extent indicated has been received from her/his employer.
•	I am prepared to have the project carried out in my organisation under the circumstances set out by the participant(s).
•	The amount of time that the investigator/s will be devoting to the project is appropriate to existing workloads.
•	The project can be accommodated within the general facilities in this organisation, and sufficient working and office space is available for any proposed additional staff.
•	All funds for this project will only be spent for the purpose for which they were provided.
•	The project will not be permitted to proceed until appropriate ethical clearance has been obtained.
•	I will notify the ARC if there are changes to named personnel after the submission of this Proposal.
•	I consent, on behalf of the participants, to this Proposal being referred to third parties for assessment purposes who will remain anonymous.
•	For any Fellowship candidate on this Proposal who is seeking a second ARF/QEII or APF Fellowship, I have agreement from the Administering Organisation for the project on which the current Fellowship is held, as well as the Fellowship candidate, that the current Fellowship will be relinquished if this Fellowship candidate is successful.
•	To the best of my knowledge, the Privacy Notice appearing at the top of this Application Form has been drawn to the attention of all the participants whose personal details have been provided at Part B.
•	To the best of my knowledge all details in this Proposal are true and complete and that no information specifically relating to personnel track or publication records is false or misleading.
•	I understand that it is an offence under the Criminal Code Act 1995 to provide false or misleading information.

Signature of DVC/PVC(R) or delegate or equivalent (in black ink)		Name and Title (please print)		Date	

			

PART B—PERSONNEL

B1	PERSON NUMBER	1	

B2	ABBREVIATED DETAILS
GAMS ID	X00392	

Family name	Drummond	Role	CI	
First name	Peter	Second name	David	
Title	Prof	
Department/school/other	Department of Physics	
Organisation	The University of Queensland	

B3	POSTAL ADDRESS
Department/school/other	Department of Physics	
Organisation	The University of Queensland	
Postal address line 1		
Postal address line 2		
Locality	Brisbane	State	QLD	Postcode	4072	Country	Australia	

B4	MEMBERSHIPS/ASSOCIATIONS
B4.1	Are you a current member of the ARC or its advisory committees?		         Yes      No  X

B4.2	Are any of your relatives or close social/professional associates members 
of the ARC or its advisory committees?                                                                        Yes      No  X
If Yes, name of the ARC member(s)	 	

B4.3 a) Are you associated with a Commonwealth Government-funded Research Centre?  Yes  X    No  
	 
If Yes: 
i) The full name of the Centre; and 	
Australian Centre of Excellence for Quantum-Atom Optics	

6/2003

	    ii) The date that funding commenced, or will commence for the 
	    Centre.

0%

iii) The percentage of your salary received from the Centre 
(to the nearest whole percent): 	

Note1, a letter from the Centre Director which describes the relationship between the proposed research and the projects funded by the Centre, and states that “the proposed research does not duplicate work that is already funded or could reasonably be expected to be funded by the Centre”, must be attached.
Note2, if the Centre has not yet commenced funding, please enter the anticipated commencement date, however a letter from the Centre director is not required.

b) Are you seeking a Fellowship, which would be hosted within a Centre?                Yes      No  X

B5	HAVE YOU BEEN AWARDED A CURRENT OR PREVIOUS ARC FELLOWSHIP 	Yes   X   No  
Project ID	Funding commencement year	Finish year	Fellowship type	
DP0210745	2002	2007	APF	

B6	AFFILIATIONS
If you are nominated as a Chief Investigator, are you currently drawing salary from a non-higher education sector organisation that is primarily funded for research from Commonwealth or State Government sources? 
                                                                                                                                                        Yes      No  X

B7	QUALIFICATIONS
B7.1	PhD qualification awarded
Discipline/Field	Physics	
Organisation	UNiversity of Waikato	
Country	NZ	
Month and Year awarded	06/1979	(or) Date Thesis Submitted/ Proposed Submission Date 		

B7.2	Other qualifications (including highest Qualification if not PhD)
Degree/Award	Year	Discipline/Field	Organisation and country	
A.M.	1973	Physics	Harvard University, USA	
B. Sc (Hons)	1970	Physics/Maths	Auckland University, NZ	

B8	ACADEMIC, RESEARCH, PROFESSIONAL AND INDUSTRIAL EXPERIENCE
B8.1	Current and previous appointment(s)/position(s) - covering a maximum of the past 10 years
Position held	Organisation	Department	Year appointed and status	
Professor	The University of Queensland	Physics	1988, Continuing	

B8.2 	Do you or will you be employed by, or hold an adjunct or equivalent appointment with, an Eligible Organisation as at 1 January 2007?				  		Yes  X    No  
If Yes, the organisation at which it is, or will it be, held:	The University of Queensland	

B9	ADDITIONAL FELLOWSHIP DETAILS (not applicable) 

This page serves as a check list for PART B10
Once the Application Form has been printed, replace this page with the following pages:

B10	RESEARCH RECORD RELATIVE TO OPPORTUNITIES
Using the headings below, on separate sheets, describe your contributions to research and research training.

Please keep all parts of Section B10 for each participant grouped together.

B10.1	A statement on your most significant contributions to this research field
Write a maximum of half an A4 page.

B10.2	All refereed publications in the past 5 years (2001 onwards)
Use asterisks to identify publications relevant to this Proposal.

B10.3	Ten career-best publications

B10.4	Other evidence of impact and contributions to the field
For example, patents, honours and awards, other professional activities.  
Write a maximum of half an A4 page.

B10.5	Any aspects of your career or opportunities for research that are relevant to assessment and that have not been detailed elsewhere in this Proposal
For example, interruptions to career, any other circumstances that may have slowed down your research and publications.

Write a maximum of half an A4 page.

B10.6	Fellowship candidates only (All Fellowships candidates may complete this section including those that are sole investigators)
In no more than one A4 page, provide details of 
a)	the contribution you will make to the project (such as your experience, skills and expertise and how they will be applied) and
b)	the research environment, that is, the facilities and support at your host organisation, including the intellectual environment.
c)	reasons for not moving to another organisation if you intend to remain at your current organisation.

PART C—PROJECT COST

Costs should be quoted exclusive of the GST.

C1	BUDGET DETAILS
C1.1	Year	1	
	COSTING	
Column 1	2	3	4	5	
    Source of funds	ARC	University	Other	Total	
DIRECT COSTS					
Personnel (Salaries + On-costs)					
Postdoc Salary	77030	0	0	77030	
 Chief Investigator Salary	0	38400	0	38400	
Total Personnel (a)	77030	38400	0	115430	
Teaching Relief					
Teaching relief - Chief Investigator	32294	0	0	32294	
Total Teaching Relief (b)	32294	0	0	32294	
Equipment					
PowerMac	3518 	0 	0 	3518 	
20" LCD Screen	1098 	0 	0 	1098 	
Total Equipment (c)	4616	0	0	4616	
Maintenance					
General maintenance 	300 	0 	0 	300 	
Total Maintenance (d)	300	0	0	300	
Travel					
International Conferences 	11148 	0 	0 	11148 	
Local Research Travel 	4287 	0 	0 	4287 	
Total Travel (e)	15435	0	0	15435	
Other					
Total Other (f)	0 	0 	0 	0 	
TOTAL DIRECT COSTS (g)	129675 	38400 	0 	168075 	
INDIRECT COSTS					
CIs, PIs and any researcher Level A or above x multiplier					
Postdoc Indirect Costs     (.092 multiplier)		70868 	0 	70868 	
TOTAL INDIRECT COSTS (h)		70868 	0 	70868 	
TOTAL COSTS (i)	129675 	109268 	0 	238943 	

C1	BUDGET DETAILS
C1.2	Year	2	
	COSTING	
Column 1	2	3	4	5	
    Source of funds	ARC	University	Other	Total	
DIRECT COSTS					
Personnel (Salaries + On-costs)					
Postdoc Salary	77030	0	0	77030	
 Chief Investigator Salary	0	38400	0	38400	
Total Personnel (a)	77030	38400	0	115430	
Teaching Relief					
Teaching relief - PI	32294	0	0	32294	
Total Teaching Relief (b)	32294	0	0	32294	
Equipment					
Laptop	2814 	0 	0 	2814 	
Total Equipment (c)	2814	0	0	2814	
Maintenance					
General maintenance 	300 	0 	0 	300 	
Total Maintenance (d)	300	0	0	300	
Travel					
International Conferences 	11148 	0 	0 	11148 	
Local Research Travel 	4287 	0 	0 	4287 	
Total Travel (e)	15435	0	0	15435	
Other					
Total Other (f)	0 	0 	0 	0 	
TOTAL DIRECT COSTS (g)	127873 	38400 	0 	166273 	
INDIRECT COSTS					
CIs, PIs and any researcher Level A or above x multiplier					
Postdoc Indirect Costs     (.92 multiplier)		70868 	0 	70868 	
TOTAL INDIRECT COSTS (h)		70868 	0 	70868 	
TOTAL COSTS (i)	127873 	109268 	0 	237141 	

C1	BUDGET DETAILS
C1.3	Year	3	
	COSTING	
Column 1	2	3	4	5	
    Source of funds	ARC	University	Other	Total	
DIRECT COSTS					
Personnel (Salaries + On-costs)					
Postdoc Salary	77030	0	0	77030	
 Chief Investigator Salary	0	38400	0	38400	
Total Personnel (a)	77030	38400	0	115430	
Teaching Relief					
Teaching relief - PI	32294	0	0	32294	
Total Teaching Relief (b)	32294	0	0	32294	
Equipment					
Quad PowerMac	4662 	0 	0 	4662 	
20" LCD Screen	1098 	0 	0 	1098 	
Total Equipment (c)	5760	0	0	5760	
Maintenance					
General maintenance 	300 	0 	0 	300 	
Total Maintenance (d)	300	0	0	300	
Travel					
International Conferences 	11148 	0 	0 	11148 	
Local Research Travel 	3287 	0 	0 	3287 	
Total Travel (e)	14435	0	0	14435	
Other					
Total Other (f)	0 	0 	0 	0 	
TOTAL DIRECT COSTS (g)	129819 	38400 	0 	168219 	
INDIRECT COSTS					
CIs, PIs and any researcher Level A or above x multiplier					
Postdoc Indirect Costs     (.092 multiplier)		70868 	0 	70868 	
TOTAL INDIRECT COSTS (h)		70868 	0 	70868 	
TOTAL COSTS (i)	129819 	109268 	0 	239087 	

This page serves as a check list for PART C2 and C3

Once the Application Form has been printed, replace this page with the following pages:

C2	JUSTIFICATION OF FUNDING REQUESTED FROM THE ARC

In no more than two A4 pages fully justify in terms of need and cost, each budget item requested from the ARC (Column 2 in Section C1).  Use the same headings as in Column 1 of Section C1.

C3	DETAILS OF NON-ARC CONTRIBUTIONS

In no more than one A4 page provide an explanation of how non-ARC contributions (Columns 3 and 4 in Section C1) will support the Proposal (use the same headings as in Column 1 of Section C1).  Contributions from Partner Investigators must be highlighted.

PART D—RESEARCH SUPPORT

D1	RESEARCH SUPPORT OF ALL PARTICIPANTS

Details provided for all participants listed in Section A3—
•	The current Proposal is listed first and will be auto populated into the table. List other Proposals and/or projects in descending date order.
•	ARC-funded projects for which reports (including Progress and Final Reports) required in the Conditions of Grant/Funding Contract/Funding Agreement have been submitted should be indicated by a double asterisk (**) after the Description.
•	Asterisk (*) refers to any items that are in the same area of research as this Proposal.
•	Support types (Sup type) are ‘C’ for current support, ‘R’ for requested support, ‘P’ for past support.
•	The ARC Project ID applies only to Proposals, current and past projects funded by the ARC.
Note, details should be provided for all sources of funding, not just ARC funding. 

Description
(All named investigators on any Proposal or grant on which a participant is involved, project title, source of support, scheme)	
(*)	
Sup type	ARC 
Project ID 

(if applicable)	
2005
($’000)	
2006
($’000)	
2007
($’000)	
2008
($’000)	
2009
($’000)	
Simulating  viral evolution and genetic complexity 	*	R	DP0773445			129	127	129	
 Bachor, Wilson, Baldwin, Close, Hope, Klshar, Lam, Osrovskaya, Savage, Truscott, Corney, Davis Drummond, Kheruntsyan, Reid, Dalton, Hannaford, Kieu, McLean, Rowlands, Sidorov, Leurchs, Ertmer, Fabre, Vassen, Wilson, Carmichael, Ballagh, Hinds, Giacobino. ARC Centre of Excellence in Quantum-Atom Optics, ARC   		C	CEO348178 	2190	2190	2190			
Drummond, `Computational Quantum Dynamics of Atom Lasers', ARC, APF grant   		C	DP0210745 	70	70				

This page serves as a check list for PART D2

Once the Application Form has been printed, replace this page with the following page(s) (where appropriate):

D2	STATEMENTS ON PROGRESS OF ARC-FUNDED PROJECTS
Include with the Proposal a statement detailing progress for each project held by any of the participants listed in Section A3 who were allocated funds for 2005 under any ARC Discovery Projects or Linkage Projects scheme.

D2.1	List of the projects that you are providing statements for
E.g.
Project ID	First named investigator	Scheme	
DP0212345	Bloggs, J 	DP	
LP0312345	Smith, C	LP	

D2.2	Provide the statements
Write no more than one A4 page for each funded project.

This page serves as a check list for PART E

Once the Application Form has been printed, replace this page with the following pages:

PART E—PROPOSAL DESCRIPTION

Please provide the following information in no more than 10 A4 pages and in the required format.

E1	PROPOSAL TITLE
Use the same title as in Section A2.

E2	AIMS AND BACKGROUND
Describe the aims and background to the Proposal.  Include information about recent international progress in the field of the research, and the relationship of this Proposal to work in the field generally.  Refer only to refereed papers that are widely available to national and international research communities.

E3	SIGNIFICANCE AND INNOVATION
Describe how the research is significant and whether the research addresses an important problem.  Describe how the anticipated outcomes will advance the knowledge base of the discipline and why the Proposal aims and concepts are novel and innovative.  Detail what new methodologies or technologies will be developed.

E4	APPROACH AND METHODOLOGY
Outline the conceptual framework, design and methods and demonstrate that these are adequately developed, well integrated and appropriate to the aims of the Proposal.

E5	NATIONAL BENEFIT
Describe the expected outcomes and the likely impact of the proposed research.  Describe how the research Proposal might result in economic, environmental and/or social benefits for Australia.

E6	COMMUNICATION OF RESULTS
Outline plans for communicating the results of the Proposal to other researchers and the broader community.

E7	ROLE OF PERSONNEL
Summarise the role, responsibilities and contributions of each Chief Investigator, Fellow and Partner Investigator.  Summarise the roles and levels of involvement of other participants, such as technical staff. 

Fellowship candidates who are neither Australian citizens nor residents should provide a statement demonstrating the special skills that they would bring to research in Australia.

E8	REFERENCES
Include a list of all references within the page limit of 10 A4 pages. This list must be in at least 10 point font.