PhD Position in Computer Science/Cheminformatics
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We are looking for PhD candidates to join the TACsy (Training Alliance for Computational Systems Chemistry) Marie-Skłodowska-Curie Joint Doctoral Network. This network consists of fifteen (15) highly interlinked PhD projects, of which this particular call is for project DC 10 Design of Multienzyme Cascades Based on Declarative Descriptions: Novel Computational Approaches. The application deadline is 2 May 2023. The anticipated start date is 1 September 2023, but flexibility in both directions is possible.
Declarative approaches to solve design and optimization problems are well established in computer science: one does not aim at specifying how a solution is implemented, but one rather specifies what an overall goal should be and the solution is then automatically computed. Such approaches have a large potential for computational chemistry, and in particular for the design of multienzyme cascades: conceptually enzymes define formal graph transformation rules, which can be used to computationally expand chemical spaces. The declarative approaches can subsequently be used to identify efficient reaction cascades (i.e. sequences of graph transformation rules). Such multi-enzymatic cascade reactions, i.e. the combination of several enzymatic transformations in one pot, have in chemistry proven to possess considerable advantages compared to classical synthesis. For instance, it is possible to reduce costs, to allow for overall reactions that would otherwise not be possible, and to reduce the concentration of harmful or unstable compounds.
In this project, the PhD candidate will focus on computational and declarative approaches to model and solve multi-enzymatic cascade design problems. Among the chemical aspects to model and optimize for are: allosteric regulation of enzymes, competitive inhibition of the active sites, cofactor recycling, switching between different operation modes, and overall autocatalytic behaviour. The candidate will develop such approaches and conduct extensive in-silico testing. We aim to compare and evaluate the computational tools developed in this project against wet-lab data produced in other projects of TACsy. The student will have a three-months research stay with our industry partner (Fluigent) focusing on microfluidics and lab-on-a-chip technologies.
We are seeking an excellent and highly motivated individual with either a Master’s degree in computer science, applied mathematics, or in chemistry, or a degree from a related field (preferably with a focus on computational methods). The ideal candidate has familiarity with one or more of the following areas: optimization, declarative approaches, algorithmics, graph theory, algorithm engineering, computational chemistry. Proven competences in programming and ease with formal thinking are a necessity.
The TACsy consortium encompasses 11 partners across six countries in Europe and North America, including both academic institutions and industrial partners. The consortium consists of world-class scientists with competences spanning chemistry, biochemistry, computer science, and machine learning. All fifteen doctoral candidates will work with two research groups, and will obtain a degree from both host institutions, and complete research stays either at world-leading industry partners or at prestigious non-European academic partners:
The candidates will all be part of a strong joint PhD training programme, with a focus on career development, application writing, communication skills, and community building through scientific summer schools.
All candidates will be expected to:
See details about the network as a whole, its scientific content, and the application and selection process here.
These positions are subject to the entry into force of grant agreement no 101072930 by and between the European Research Executive Agency and University of Southern Denmark and thereby funded by the European Union’s Horizon Europe Research and Innovation Programme.
Application, salary etc.
The guaranteed Doctoral Candidate PhD funding from the European Commission is for 36 months. Therefore, appointment as a PhD research fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period. Additional funding may be possible, depending on the local supervisor and in accordance with the regular PhD time in the country of origin.
All positions are fully funded, with very competitive salaries. More information on funding from the MSCA programme can be found here (beginning on page 78). Please note a country correction coefficient (page 109) applies to the living allowance in order to ensure equal treatment and purchasing power parity for all researchers. Salary rules apply to the doctoral candidates hosted in the European Union and will change depending on the host institution.
The TACsy project wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. We are searching for a diverse group of candidates with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisations and to have the same career opportunities. The position of working hours is flexible in order to accommodate individual needs and allow for the best possible work-life balance for each candidate.
Application must be in English and must include the following:
Applications must be submitted electronically using the link “Apply online”. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.
Details on the selection timeline and process can be found at the TACsy homepage. Please note that the recruitment team reserves the right to conduct a second interview. Shortlisting may be used in the assessment process.
Please note that there are two limitations to apply for this programme, as specified in the MSCA regulations. Applicants must:
Contact Information
For further information please contact Daniel Merkle, tel.: +45 6550 2322, e-mail: [email protected].
Send application
Deadline: 2 May 2023.
You can apply for the job at Faculty of Science by completing the application form.
Further information about the PhD-study at the University of Southern Denmark (SDU) can be found at the homepage of the University.
The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations), if employed at SDU.
The successful candidate will, if employed at SDU, be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).
Further information for international applicants considering applying for a job at SDU. Please take a look at the webpage from the International Staff Office (ISO) at SDU.
Declarative approaches to solve design and optimization problems are well established in computer science: one does not aim at specifying how a solution is implemented, but one rather specifies what an overall goal should be and the solution is then automatically computed. Such approaches have a large potential for computational chemistry, and in particular for the design of multienzyme cascades: conceptually enzymes define formal graph transformation rules, which can be used to computationally expand chemical spaces. The declarative approaches can subsequently be used to identify efficient reaction cascades (i.e. sequences of graph transformation rules). Such multi-enzymatic cascade reactions, i.e. the combination of several enzymatic transformations in one pot, have in chemistry proven to possess considerable advantages compared to classical synthesis. For instance, it is possible to reduce costs, to allow for overall reactions that would otherwise not be possible, and to reduce the concentration of harmful or unstable compounds.
In this project, the PhD candidate will focus on computational and declarative approaches to model and solve multi-enzymatic cascade design problems. Among the chemical aspects to model and optimize for are: allosteric regulation of enzymes, competitive inhibition of the active sites, cofactor recycling, switching between different operation modes, and overall autocatalytic behaviour. The candidate will develop such approaches and conduct extensive in-silico testing. We aim to compare and evaluate the computational tools developed in this project against wet-lab data produced in other projects of TACsy. The student will have a three-months research stay with our industry partner (Fluigent) focusing on microfluidics and lab-on-a-chip technologies.
We are seeking an excellent and highly motivated individual with either a Master’s degree in computer science, applied mathematics, or in chemistry, or a degree from a related field (preferably with a focus on computational methods). The ideal candidate has familiarity with one or more of the following areas: optimization, declarative approaches, algorithmics, graph theory, algorithm engineering, computational chemistry. Proven competences in programming and ease with formal thinking are a necessity.
The TACsy consortium encompasses 11 partners across six countries in Europe and North America, including both academic institutions and industrial partners. The consortium consists of world-class scientists with competences spanning chemistry, biochemistry, computer science, and machine learning. All fifteen doctoral candidates will work with two research groups, and will obtain a degree from both host institutions, and complete research stays either at world-leading industry partners or at prestigious non-European academic partners:
- University of Southern Denmark (DK)
- University of Vienna (AT)
- Leipzig University (DE)
- Friedrich-Schiller-University Jena (DE)
- TU Vienna (AT)
- The University of Sheffield (UK)
- European Molecular Biology Laboratory (EMBL)
- BASF SE (DE)
- Fluigent SA (FR)
- Thermo Fisher Scientific GMBH (DE)
- Harvard Medical School (US).
The candidates will all be part of a strong joint PhD training programme, with a focus on career development, application writing, communication skills, and community building through scientific summer schools.
All candidates will be expected to:
- Have potential for conducting outstanding research, as demonstrated by scientific accomplishments (in particular quality of thesis, but also e.g. code repositories, conference presentations, outreach activities, or publications).
- Be interested in working in a multidisciplinary and international research environment.
- Have excellent communication skills in English, verbally as well as in scientific writing.
- Be willing to undertake international research stays, internships, and travels.
See details about the network as a whole, its scientific content, and the application and selection process here.
These positions are subject to the entry into force of grant agreement no 101072930 by and between the European Research Executive Agency and University of Southern Denmark and thereby funded by the European Union’s Horizon Europe Research and Innovation Programme.
Application, salary etc.
The guaranteed Doctoral Candidate PhD funding from the European Commission is for 36 months. Therefore, appointment as a PhD research fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period. Additional funding may be possible, depending on the local supervisor and in accordance with the regular PhD time in the country of origin.
All positions are fully funded, with very competitive salaries. More information on funding from the MSCA programme can be found here (beginning on page 78). Please note a country correction coefficient (page 109) applies to the living allowance in order to ensure equal treatment and purchasing power parity for all researchers. Salary rules apply to the doctoral candidates hosted in the European Union and will change depending on the host institution.
The TACsy project wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. We are searching for a diverse group of candidates with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisations and to have the same career opportunities. The position of working hours is flexible in order to accommodate individual needs and allow for the best possible work-life balance for each candidate.
Application must be in English and must include the following:
- A research proposal/description of your approach to the project in question (max one page excluding references) should be attached under the “Project description” option.
- A letter stating your specific interest, motivation and qualifications for the project. (max. two pages) should be attached under the “Application form” option.
- Detailed CV, including personal contact information of two or three references, should be attached under the “CV” option.
- Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades. This should be collated into one document and attached under the “Certificates” option. Please note that some positions may have specific requirements for their PhD School admission, such as 60 ECTS MSc courses completed or a full MSc degree. These are listed in each position description.
- At least two signed reference letters, combined into one file and attached under the “References” option. Should your referees wish to send their letters directly to us, please have them sent to [email protected] and mention your name and the title of the position in the subject line. And please note that these also need to reach us before the deadline.
Applications must be submitted electronically using the link “Apply online”. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.
Details on the selection timeline and process can be found at the TACsy homepage. Please note that the recruitment team reserves the right to conduct a second interview. Shortlisting may be used in the assessment process.
Please note that there are two limitations to apply for this programme, as specified in the MSCA regulations. Applicants must:
- Not be in possession of a PhD degree at the date of recruitment.
- Meet the Marie-Curie mobility rule (see pages 84-85 here). In TACsy, this means the applicants are not eligible for a specific position if it is true for both host institutions of the position that the applicant for more than 12 of the last 36 months have resided or performed a main activity (work, studies, etc.) in the country of that host institution. The host institutions relevant to this rule are located in Austria and Denmark.
Contact Information
For further information please contact Daniel Merkle, tel.: +45 6550 2322, e-mail: [email protected].
Send application
Deadline: 2 May 2023.
You can apply for the job at Faculty of Science by completing the application form.
Further information about the PhD-study at the University of Southern Denmark (SDU) can be found at the homepage of the University.
The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations), if employed at SDU.
The successful candidate will, if employed at SDU, be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).
Further information for international applicants considering applying for a job at SDU. Please take a look at the webpage from the International Staff Office (ISO) at SDU.
Information og data
Denne ledige stilling har jobtypen "Forsker", og befinder sig i kategorien "Sundhed og forskning".
Arbejdsstedet er beliggende i Hele Danmark
Jobbet er oprettet på vores service den 31.3.2023, men kan have været deaktiveret og genaktiveret igen.
Dagligt opdateret: Dette job opdateres dagligt ud fra jobudbyderens hjemmeside via vores søgemaskineteknologi og er aktivt lige nu.
- Forsker
- Tirsdag den 02. maj 2023
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