Molecular Simulation Software Scientist (KTP associate) University of Edinburgh, School of Chemistry, University of Edinburgh and Cresset United Kingdom

Molecular Simulation Software Scientist (KTP associate)

Vacancy Ref: : 043722

Closing Date : 07-Jun-2018

Contact Person : Dr Julien Michel

Contact Number : N/A

Contact Email :

The University of Edinburgh (UoE) and Cresset are recruiting a postdoctoral level scientist to lead on a collaborative project to develop a user-friendly software for molecular simulations-driven computer-aided drug design. The position is based at Cresset’s offices in Cambridgeshire. Cresset provides computational drug design software and services to the life sciences market. This is an exciting opportunity for a computational scientist wishing to pursue a career in the life-sciences software industry.


The post will involve a review of the current use of free energy perturbation methods (FEP) at UoE, deployment of academic software on Cresset infrastructure and benchmarking for software validation, integration of academic FEP software into Cresset’s commercial offerings, automation of individual steps of the workflow, beta release of software, large scale validation and commercialisation activities.


Fixed Term: 15 months fixed term from 01 July 2018.


1. Job Details

Job title: Molecular simulation software scientist (KTP associate)
School/Support Department: School of Chemistry, University of Edinburgh and Cresset
Line manager: Dr Julien Michel (University of Edinburgh) and Dr. Mark Mackey (Cresset)


2. Job Purpose

This project is supported by Innovate UK. The aim of this project is to develop a user friendly interface for molecular simulations driven computer-aided drug design. The post-holder will review the current use of free energy perturbation methods (FEP) at UoE. Activities will include deployment of academic software developed in the Michel lab on Cresset infrastructure and benchmarking for software validation, integration of academic FEP software into Cresset’s commercial offerings, automation of individual steps of the workflow, beta release of software, large scale validation and commercialisation activities


The position is based at Cresset’s headquarters in Cambridgeshire. The post holder will be expected to interact regularly with other members of the Michel research group, the School of Chemistry, and external collaborators.


3. Main Responsibilities (Approx % of Time)

To review current use of free energy perturbation methods in academia and industry. To deploy academic software developed by the Michel lab and other labs on Cresset infrastructure. To carry out benchmark studies for software validation. To integrate various piece of academic software into Cresset’s commercial offerings. To automate and validate individual steps of a FEP workflow. To contribute to software releases, large scale validation studies and commercialisation activities. (80%)


To attend KTP associate training activities provided by InnovateUK. (10%)


To travel and meet with customers. (10%)


4. Planning and Organising

As required for the completion of Main Responsibilities.


5. Problem Solving

Critical thinking and problem solving as relevant to completion of Main Responsibilities, specifically focussing on problem solving with respect to:
(a) Troubleshooting technical issues.
(b) Collaboration with other team members.
(c) Development of relationships with our external partners.


6. Decision Making

Independent decision making as part of day-to-day operations and decision making in conjunction with PIs concerning major developments.


7. Key Contacts/Relationships

Principle Investigators: Dr Mark Mackey (Cresset) and Dr Julien Michel (UoE)
Your key contacts will include:
Within the School – Members of the Michel research group
Outwith the University – Members of Cresset


8. Knowledge, Skills and Experience Needed for the Job

Essential Criteria

• PhD in computational chemistry or related discipline.
• Proven expertise in use of modern biomolecular simulation software suites (e.g. Amber, Gromacs, OpenMM, Sire).
• Proven ability to write custom software using scripting languages such as Python.
• Strong written and oral communication skills as evidenced by scientific publications in relevant journals and presentations at relevant scientific meetings.


Desirable Criteria
• Post-doctoral research experience (1-2 years) validating the Associate’s ability to deliver results in different work environments.
• Expert knowledge of the theory behind molecular simulations.
• Proven software engineering skills as evidenced by use of version control software, collaborative development of large pieces of scientific software, provision of technical documentation and/or training workshops.
• Expertise in C++ programming.


Specific Qualities
• Collaborative and team-player.
• Ability to work independently.
• Ability to work under pressure and meet deadlines.
• Willing to travel to meet customers.


9. Dimensions

You will be part of a team of a dozen computational scientists providing software and consultancy services to the pharmaceuticals, biotech and chemicals sectors. You will interact with academic staff, researchers and students at the School.


10. Job Context and any other relevant information


Enhanced Package

As part of the project an enhanced professional development package (business skills training) will be provided.


Application Procedure

All applicants should apply online by clicking the apply link at the bottom of this page and submitting an up to date CV. The application process is quick and easy to follow, and you will receive email confirmation of safe receipt of your application. The online system allows you to submit a CV and other attachments.


We anticipate interviews will be held in 3 weeks after the closing date. You will be notified by email whether you have been shortlisted for interview or not.


The closing date is 5pm GMT on 07 June 2018.


Eligibility to Work

In accordance with the Immigration, Asylum and Nationality Act 2006 and Immigration Act 2016 the University of Edinburgh, as an employer, has a legal responsibility to prevent illegal working and therefore must check that all employees are entitled to work in the United Kingdom (UK).


To do so, the University of Edinburgh requires to see original documents evidencing right to work in the UK before commencement of employment and this is normally carried out at interview. Details will be provided in any letter of invitation to interview.


For further information on eligibility to work please visit our eligibility to work webpage


If you are from outside the EEA and not currently eligible to work in the UK, there are visa routes that may be available to you, for example:


Tier 1 (Exceptional Talent): If you are an academic in the field of sciences; humanities; engineering; medicine; digital technology; or the arts, it may be possible for you to apply for a Tier 1 (Exceptional Talent) visa. This route requires you to apply to be endorsed as an internationally recognised leader or emerging leader in your particular field by a designated competent body (Arts Council England, British Academy, Royal Academy of Engineering, Royal Society, Tech City UK). However, if you are applying for a senior academic role, e.g. Professor/Reader there is an accelerated route to endorsement. Further information can be found on the UKVI website

Tier 2: The University is a UKVI licensed sponsor and is able to issue a Certificate of Sponsorship (CoS) to successful candidates who are offered highly skilled roles and meet the eligibility criteria. The CoS enables candidates to apply for a Tier 2 (general visa).
Further information about whether you require a visa and other visa routes can be found at:


Conditions of Employment

Pension Scheme

This role is grade UE07 and therefore the post holder is automatically included in membership of the Universities Superannuation Scheme (USS), subject to the USS membership criteria, unless they indicate that they choose not to join the Scheme.

For further information please visit our Pensions website.



The role is grade UE07 and attracts an annual salary of £32,548 to £38,833 for 35 hours each week. Salary is paid monthly by direct transfer to your Bank or Building Society account, normally on the 28th of the month. Salaries for part-time staff are calculated on the full-time scales, pro-rata to the Standard Working Week.


The University reserves the right to vary the candidate information or make no appointment at all. Neither in part, nor in whole does this information form part of any contract between the University and any individual.


The School of Chemistry

The School of Chemistry at the University of Edinburgh has a long and distinguished history. The first Chemistry Professor was appointed to the Chair in 1713 and the Edinburgh University student-led Chemical Society is regarded as the oldest chemical society in the world. The School is run as a single academic unit with approximately 50 academic staff, 40 professional support staff and 250 research students and post-doctoral workers and a first year intake of 135 Chemistry undergraduates. The School of Chemistry at Edinburgh holds a Gold Athena SWAN award, in recognition of excellence in science, engineering and technology employment in higher education relating to supporting women in Science.


Research and EaStCHEM

In the latest Research Excellence Framework (REF 2014) ‘Power Table’, EaStCHEM, the joint research school of Edinburgh and St Andrews Chemistry departments, is ranked the 2nd best Chemistry Department in the UK, and 1st in Scotland. Overall, 95 % of our research is classed as world leading or internationally excellent and the EaStCHEM research School has grown to over 80 academics (99% of which were submitted to REF), a testament to both the breadth and strength of our research. More specifically, 100 % of our research environment, which includes factors such as our facilities, grant income, and awards and prizes, is rated as 4* or 3*, and more than 95 % of our research papers submitted for the exercise have been rated as 4* or 3*.


Chemistry at the University of Edinburgh has over £34M of current research grants, and has an international research reputation with many of our staff holding prestigious national and international awards. This world-class centre for chemistry has four research groupings: the Chemistry/Biology Interface; Experimental and Theoretical Chemical Physics; Molecular Synthetic Chemistry; and Materials Chemistry. Many academics are involved in more than one research area, and this breadth of activity is exemplified by our research collaborations with our EaStCHEM partner across a variety of disciplines.


We have world class facilities across the breadth of Chemistry with ready access for all researchers. The provision of an excellent equipment base and service infrastructure underpins all of the research within EaStCHEM, and our core strategy is to ensure the complementarity and synergy between the EaStCHEM partners. Each has a suite of analytical equipment that can be regarded as essential infrastructure for every top-class Chemistry Research School and dedicated scientific support. These facilities include recently refurbished laboratories, a full suite of high- and low-field NMR instrumentation, mass spectrometry, single crystal and powder X-ray crystallography, magnetometry, EPR spectroscopy, surface science, thermal analysis and porosimetry, optical spectroscopy, high pressure facilities, fermentation suite, DNA synthesis, protein purification and biophysical facilities, and the EaStCHEM Research Computing Facility. These are coupled with specialised units where cutting-edge characterisation work is led by world-leading scientists. We also work with developers of national facilities in the UK (Diamond, RAL), Europe (ESRF, ILL), USA (ALS, APS, Oak Ridge, NIST) and further afield in, for example, Australia (ANSTO) and Japan (Spring-8).


We also have dedicated in-house business development executives that manage a large portfolio of research and consultancy projects involving industrial partners, and who offer a variety of services from analysis, consultancy, collaborative research, KTP and R&D support to Industrial sponsored projects. Our research staff work closely with the BDEs and with the local University Commercialisation Offices to ensure that industrial engagement activities and IP development opportunities are maximised.

College of Science and Engineering (

The College of Science and Engineering (CSE) is one of the largest and highest-ranked science and engineering groupings in the UK. Headed by Professor Dave Robertson, CSE comprises seven Schools (Biological Sciences, Chemistry, Engineering, GeoSciences, Informatics, Mathematics, and Physics and Astronomy). Informatics is located in the University’s Central Area near George Square, with the other six 2 miles further south at the King’s Buildings. The College has over 3,000 academic and support staff, and educates some 6,000 undergraduates, over 1000 taught postgraduates and more than 2,000 research students. It is in the front rank of UK university science and engineering groupings for research quality and income, and is a key player in many European and international research collaborations.


Research Excellence Framework (REF) 2014


In the 2014 REF over 95% of our staff were submitted. Of our seven submissions, four of which were as a joint research school in combination with a strategic research university partner through pooling, 3 were ranked top in the UK and all 7 were in the top 5 in their discipline in the Times Higher Power rankings.

The University of Edinburgh

For more than four centuries, our people and their achievements have rewritten history time and again. They’ve explored space, revolutionised surgery, published era-defining books, paved the way for life-saving medical breakthroughs and introduced to the world many inventions, discoveries and ideas from penicillin to Dolly the sheep. We have believed that anything is possible, we still do.

The latest Research Excellence Framework highlighted our place at the forefront of international research. This adds to our international reputation for the quality of our teaching and our student experience excellence. The University is proud of its success with online teaching initiatives, with 2550 students currently studying its online distance learning postgraduate programmes, and a total to date of more than 2 million enrolments for Edinburgh MOOCs.


As a member of staff, you will be part of one of the world's leading universities, with 20 Schools spread over 3 Colleges that offer more than 1600 undergraduate and 600 postgraduate programmes to over 35,000 students each year. Professional services are critical to this success as well as our world-class teaching, research and student facilities. In fact, we are one of the top employers in Edinburgh, with over 13,000 people spread across a wide range of academic and supporting roles.


As a world-changing, world-leading university, we offer an exciting, positive, creative, challenging and rewarding place to work. We give you support, nurture your talent, develop and reward success and integrate academic, professional and personal career goals, as well as give your career the benefit of a great and distinguished reputation. In addition, our employees benefit from a competitive reward package and a wide range of staff benefits, which include generous holiday entitlement, a defined benefits pension scheme, staff discounts and much more. Access our staff benefits page for further information and use our reward calculator to find out the total value of pay and benefits provided.


The University of Edinburgh holds a Silver Athena SWAN award in recognition of our commitment to advance gender equality in higher education. We are members of the Race Equality Charter and we are also Stonewall Scotland Diversity Champions, actively promoting LGBT equality. The University has a range of initiatives to support a family friendly working environment, including flexible working and childcare vouchers. See our University Initiatives website for further information.


University Family Friendly Initiatives

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

If you apply for this position please say you saw it on Physicaloxy


All Jobs







Uni Anu

Uni Copenhagen

Uni Gothenburg

Uni Kuwait

Uni Laval

Uni Nus Singapore

Uni Seoul

Uni Simon Fraser

Uni Tcd

Uni Tokio

Uni Unsw