application for a/teoretisk kemi och... · application for a doctoral programme in theoretical...

Application for a

Doctoral Programme in Theoretical Chemistry

and Biology

2010-10-29 KTH School of Biotechnology

perake

Text Box

V-2009-024669 ENG, Revised

Doctoral Programme in Theoretical Chemistry and Biology

Programme Description


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1. Programme Name Doktorsprogram i Teoretisk Kemi och Biologi Doctoral Programme in Theoretical Chemistry and Biology 2. Scientific Field Theoretical Chemistry and Biology is an interdisciplinary scientific field where physics theory, mathemathics and computational science is used to investigate, explain and predict chemical and biological phenomena and processes, including material properties. 3. Overall Goals of the Doctoral Programme in Theoretical Chemistry and Biology The overall goals of the Doctoral Programme complies with the goals for the research education that have been layed down by the faculty of KTH: The aim is to provide the society with researchers who can contribute to the development of a sustainable society. The research students shall become independent and excellent researchers. After completed studies the research student in the Doctoral Programme in Theoretical Chemistry and Biology shall be able to:

• Describe and explain theories and empirical results within the area of specialization • Formulate concrete research questions within the area of specialization • Use scientific methods and develop new knowledge through own scientific studies • Critically analyze and evaluate used methods and results from own and others scientific studies • Present and discuss research results within the scientific community • Present research in a pedagogical manner outside the scientific community and in educational situations • Valuate ethical aspects concerning research within the area of specialization and being able to act accordingly • Identify needs for new knowledge and have the ability and knowledge to initiate and lead research activities

4. Doctoral Programme. Size and Student Recruitment 4.1 Estimated number of enrolled students. Under the six-year period between 2004-2009, ten doctoral students were, on average, enrolled as new PhD students each year in the specialization area Theoretical Chemistry, in those days part of the research education subject (sv. forskarutbildningsämnet) Biotechnology. This translates to approximately 40 simultaneously active PhD students. In the planned Doctoral Programme Theoretical Chemistry and Biology, it could be expected that an increased number of students will be enrolled each year (as Biology now is more emphasized, thereby reaching out for a wider undergraduate community). However,

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the number of enrolled doctoral students will continue to be dependent on both the financial situation (faculty funding and external grants) and on available supervisor resources. 4.2 Student target groups. The target groups for the Doctoral Programme in Theoretical Chemistry and Biology are students with exams from Swedish or international undergraduate programmes, typically Master of Science programmes, in the areas of Chemistry, Physics, Biotechnology or Mathematics. A particular target are those students in mathematics and numerical analysis with interest in biological/chemical/material applications. 4.3 Admission Requirements. Eligibility to the Doctoral Programme in Theoretical Chemistry and Biology first involves the basic requirements for admission to research studies in general set forth by the Swedish Government (see "Högskoleförordningen", chapter 7, §39):

1. a completed university exam at advanced level, 2. fulfilled course requirements of at least 240 ECTS, of which at least 60 ECTS is at advanced level, or 3. corresponding merits acquired through other procedures

Further, for admission to the Doctoral Programme in Theoretical Chemistry and Biology, the completed university exam or the advanced level courses should be in a relevant subject area. In addition to these requirements, also special requirements may apply. These are in such cases described in the document "Study plan for the research education subject Theoretical Chemistry and Biology (see Appendix 1). When included, these requirements are deemed necessary for the students to profit from the training, and may for example involve knowledge/skills from university studies in particular areas of importance for the subject area or language skills. The requirements are the same for students aiming for either doctoral or licentiate degrees. 4.4 Recruitment and enrollment of research students. Recruitment, eligibility control of students will be performed according to the procedures recommended by KTH: • Advertisment policy. See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/antagning/antagningsordning-for-utbildning-pa-forskarniva-vid-kth-1.27236 • Selection criteria. See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/antagning/antagningsordning-for-utbildning-pa-forskarniva-vid-kth-1.27236 • Eligibility control process, exceptions etc. See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/antagning/antagningsordning-for-utbildning-pa-forskarniva-vid-kth-1.27236 • Main supervisor/co-supervisor(s). See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/handledning-studieuppfoljning/handledare-och-handledning-av-doktorand-1.27238

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• Financial plan. A financial plan for the first two years should be presented at the time of submission of the admission documents. 4.5 Supervisor capacity. At present four professors, two guest professors and three associate professors/senior lecturers (w. PhD exams) are active within the proposed Doctoral Programme. Also, a new senior lecturer (w. PhD exam) position is presently being appointed. Three professors at other KTH departments will particpate in the program (see Appendix 2). Thus, in total, 13 senior scientists (ten at the School of Biotechnology) will be able to operatively act as main supervisors in the Doctoral Programme of Theoretical Chemistry and Biology. In addition, other senior scientists active at the Division of Theoretical Chemistry and Biology within the School of Biotechnology, are likely to be promoted to associate professors within 5-10 years, and thus can act as main supervisors for licentiate or PhD students within the Doctoral Programme. 5. Financing 5.1 Financing of key persons in the programme. The programme responsible person will be partly (ca. 20 % of an FTE) financed by the KTH School of Biotechnology. Main supervisors and course responsible persons, including the persons included in the programme steering committee, will be financed through a mixture of faculty support and external grants. 5.2 Financing of research students. Enrolled research students are exptected to be financed mainly through external grants from various national and international sources, including The Swedish Research Council (VR), VINNOVA, EU and China Scholarship Council (CSC) as well as from industry and other private bodies (e.g. Knut and Alice Wallenberg Foundation, Wenner-Gren Foundation). In addition, the KTH School of Biotechnology has since 2008 an internal programme for appointment of "Excellence PhD students", with a background from the KTH Biotechnology education programmes. Selected students are given a four-year grant from the school to be used for the financing of a PhD student position (sw. "doktorandtjänst") with a main supervisor employed at the School of Biotechnology. At present, two/four students per year are selected, which are free to choose any main supervisor at the school. The plan is to continue this programme also after the introduction of Doctoral Programmes at the School of Biotechnology (Biotechnology and Theoretical Chemistry and Biology). 6. Courses A 240 ECTS credits doctoral degree exam comprises a course part of 60 ECTS credits and a thesis part of 180 ECTS credits. Of the 60 ECTS credits of courses included, 60 % (=36 ECTS credits) need to be research level courses. A 120 ECTS credits licentiate degree exam comprises a course part of 30 ECTS credits and a thesis part of 90 ECTS credits. Of the 30 ECTS credits of courses included, 50 % (=15 ECTS credits) need to be research level courses. Research level courses given at KTH are classified into four different categories: (A) Advanced courses (B) Research skill courses (C) Broadening courses (D) Other courses

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The Doctoral Programme in Theoretical Chemistry and Biology includes a single research education subject; Theoretical Chemistry and Biology, with no underlying specialization areas.

For the research education subject, a course package of obligatory (O) and recommended (R) courses has been assembled from the different categories of courses (A-D) (see Appendix 3). Obligatory courses should be given at least every second year. A few courses are obligatory and thus constitute common courses for the Doctoral Programme in Theoretical Chemistry and Biology. The number of ECTS credits corresponding to obligatory and conditionally obligatory courses varies between 30 and 70 % of required points, depending on if a licentiate or a doctoral degree exam is the aim. The possibility to replace an obligatory course with an equivalent course shall exist, after approval from the programme responsible person and the Director of Postgraduate Studies. There will be regularly arranged literature seminar courses in which research topics of general and broad interest are presented and discussed in a plenum, serve as an important forum for cross-disciplinary interactions, scientific and social networking and competence broadening. It will be obligatory to participate in at least one full-year round of this type of seminar series. 7. Description of the Systematic Quality Assessment Activities The goal for the systematic quality assessment work is to secure that the goals with the education are fulfilled. 7.1 Programme steering committee. A doctoral programme steering committee, consisting of the programme responsible person, the director of postgraduate studies, two to three main supervisor representatives and one research student representative will be formed which in regular meetings (approximately bi-annually) will discuss quality aspects related to particular parts of the process, incl.: - the recruitment process - supervisor competence - the course/seminar activities, incl. written evaluations - thesis quality - student throughput - employability after examination 7.2 Supervisors forum. The supervisors within a particular specialization area or a group of specialization areas are recommended to meet at least annually in a specific forum for discussions about the doctoral programme, the courses, the quality of the research, supervisor issues and the progress of the research students. 7.3 Courses and theses quality assessment. All courses are to be subject to a written evaluation. In addition to the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246), the following criteria, representing the present praxis and norm for the scientific field, should serve as guidelines related to the content and quality of doctoral and licentiate theses. Cases for

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which these guidelines for any reason are not considered applicable or relevant should be discussed with the director of postgraduate studies and the dean of KTH School of Biotechnology.

DOCTORAL THESIS Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on four papers. • Normally, two of the included papers should either be already published or formally accepted

for publication ("in press") in international peer-reviewed scientific journals. Additional papers could be included as manuscripts, preferably as "submitted for publication" to international peer-reviewed scientific journals.

• The student should appear as first author on at least two of the papers, including one of the papers belonging to the "published or in press" category.

• For any paper included, his/her contribution should be significant and clearly identifiable. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at

least one senior scientist.

• In case a thesis is based solely on manuscripts which are not already published or formally accepted for publication ("in press") in international peer-reviewed scientific journals, the thesis and the manuscripts should be pre-examined prior to printing, in addition to the main supervisor and at least one senior scientist also by the faculty opponent and the evaluation committee.

Monography thesis (sv. "monografi") • Monography theses should be avoided. KTH has the outspoken policy that research results

should be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at

least two senior scientists and the director of postgraduate studies.

LICENTIATE THESIS Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on two papers. • The included papers need not to be already published or formally accepted for publication ("in

press") in peer-reviewed international scientific journals. However, at least one manuscript should normally be included as "submitted for publication" to an international peer-reviewed scientific journal.

• The student should appear as first author on at least one of the papers included. • For any paper included, his/her contribution should be significant and clearly identifiable. • If the thesis includes one or more paper which are published or formally accepted for

publication ("in press") in an international peer-reviewed scientific journal, the thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least one senior scientist.

• If the thesis does not include any paper which is published or formally accepted for publication ("in press") in an international peer-reviewed scientific journal, the thesis shall be pre-

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examined prior to printing, in addition to the main supervisor also by at least two senior scientists.


should be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at

least two senior scientists and the director of postgraduate studies.

7.4 Assessment of the infrastructure available for students within the doctoral programme. At KTH a very resourceful new centre in CSE - the Swedish Escience Research Center (SERC) has been created as a result of the recent stategic research intitiative by the government. SERC takes national responsibility in the Escience area in terms of hosting the vast majority of Swedish Escience infrastructure through national computer centers, where PDC at KTH takes a leading role. The recent initiative by KTH to host a European PRACE system at PDC for peta flop computing is also highly relevant in the present context, as it will allow the PhD students of our program to access a world leading cutting edge hardware / software facility. The procurement of a 300 Tflop CRAY computer, in full operation from January 2010, will put KTH as leading Nordic provider of simulation power. The department has a large share of SNIC (Swedish National infrastruture) resources at national computer centers, and has large allocations of international computer power, for instance in China through the KTH-USTC center which is directed by our department. All initiatives and resources will be of immediate consequence for the execution of our Doctoral Program, Concerning the other divisions in the School of Biotechnology, two sites are available for laboratory work in joint simulation – experimental projects; the AlbaNova University Center and the KTH facilities of which the latter resides within the Science for Life Laboratory hosted in the Karolinska Science Park house (Solna). Both these laboratories represent modern laboratories appropriately equipped for biological life science experiments, involving handell ing, storage and destruction of biological material (fume hoods, temperated incubator rooms, refrigerator and freeze rooms, autoclaves etc.). In addition, the instrumental standard is relatively high, exemplified for example by instrumentation for (i) measurements of biomolecular recognition (biosensors, flow cytometers), (ii) high throughput sequencing of nucleic acids (DNA sequencers), (iii) microarray fabrication (nucleic acids and proteins) and scanning, (iv) DNA amplification (PCR instruments), (v) spectrophotometers, (vi) biosample centrifugation, (vii) biomolecule purification (chromatography equipment), (viii) mass determination (mass spectrometers) and (ix) fermentors of different scales (2 to 300 litres) for cell culturing. All PhD students are provided with an office work place, a computer and standard office facilities (printer, fax, scanner, telephone, etc.). Pentry spaces are available for cooking of own food. The KTH School of Biotechnology provides standard administrative services to PhD students, such as administration of salary payment, insurances, vacations, parental leaves, etc. A human resources (HR) responsible function is available. The services of the large KTH central library is available to all students. KTH Bio school-related research education matters are handled by both local and more central functions: • Programme responsible person • The Chemistry and Biotechnology (KKB) Office (joint facility between CHE and BIO schools)

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• The local research education administration responsible persons • The director of postgraduate studies 8. Local, National and International Networks International Connections The division of Theoretical Chemistry and Biology coordinates or participates in a large number of networks at the local, national and international levels (see Appendix 4). The lab has a strong international profile of PhD students (35 out of current 40 students are foreign), and has a long record of successful financing of PhDs through Swedish agencies like SI, SIDA, KVA, and through agencies in the home countries of the students, like CAPEC and CNPq in Brazil, China Scholarship Council, Indian Institute of Science, and through various European programs (in particular Marie Curie) which the department has coordinated or participated in.

There are strong Nordic connections; including the participation in a Nordic Network of Centers of Excellence, with exchange of students and seniors; in a Masters Educational program joining 5 Nordic Universities (start fall 2011). Further, the division is a main partner of the the Scandinavian DALTON project, with associate computer simulation program, which will be instrumental for many of course exercises. DALTON has more than 2000 license holders for which our doctoral programme will be highlighted, and which will continuously serve new students as well as alumni with cutting edge software in molecular/ multiscale modelling. Another great strategic asset for the student recruitment is inherent in the international networks the division has built. The division has strong ties with a large number of international groups in Japan, USA, and Europe, and in particular new emerging powers like China, India and Brazil. With China alone, there is a scientific and student exchange with 14 of the leading universities, including a co-directing of a KTH-China research center (KTH - USTC center in Bio- and Nano-materials). With India there are five ongoing externally funded programs, including ia trilateral KTH-India-China research center. These networks provide a very wide human resource for recruitment on all levels, including the PhD student level, and for finding career opportunities for the students after examination. Company representation and contact Exisiting company connections and support for Theo-chem-bio and other groups will be useful for the program, for instance with Astra Zeneca, ACREO, Portendo AB, BioVitrum AB, Biotage AB, LightLab Sweden AB. Meetings will be arranged where industrial researchers within the area of computational science are invited. These meetings, which also involve KTH alumni in computational science, can provide career information and opportunities for students with speciality in the subjects of our Doctor program. The meetings are organized as a series of general presentations of the industrial persons, addressing the role of computing, the policy for recruitment and collaboration with academia. Group discussions are held where the students get the opportunity to interview the industrial representatives and learn about qualified application areas that are potentially available for their future careers. Local level In the above mentioned SERC center the division is responsible for “the electronic structure community”, togheter with KTH Materials Science (Anna Delin). Further, the division is, through a newly introduced EU program SCALALIFE (Scalable Software Services for Life Science, coordinated by PDC), involved with PDC technicians for software development as well as with KTH Department of Theoretical Physics (newly inaugurated Professor Erik Lindahl) for

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co-developing multiscale (Quantum – Classical ) software for Life Science applications and with full adaption of modern multicore hardware (for instance that available through the European PetaFlop PRACE project). Furthermore, we are a founding partner of the KTH Computer Science and Engineering center (KCSE, mentioned above), involving seven KTH departments. This center will at new year 2011 be absorbed into SERC, but will maintain its trans-disciplinary doctoral programme in computer simulations, where we are responsible for several courses. Thus there will be strong synergy with this program during its remaining three years of operation. Furthermore, we are coordinating a NORDITA funded Nordic summer PhD research School in “Multiscale Modelling and Simulation in Science” which is run biannually for three weeks at the Albonova Campus. In addition to formal (i.e. agreement regulated) and repeatedly re-occuring exchange programmes with international universities associated the doctoral programme, enrolled PhD students are encouraged to visit other research groups and laboratories for different time periods, for example to learn a new technique or to perform collaborative experiments. Large EU consortia and center environments are excellent milieus for establishing networks both between academic researchers and between academic researchers and industry.

9. Connections Between the Doctoral Programme and the School Development Plan and the Rector Contract

The Doctoral Programme will use Excellence student positions as one source of financing for enrolled PhD students. The financing of these positions is in part linked to the present and future Rector Contracts (Rector Contract). The introduction of specialization area-specific course packages is in line with the long term efforts of the BIO school to secure the quality of the research education (BIO school Strategy Plan 2009-2012). The Doctoral Programme relies on senior scientists as course responsible persons and as supervisors. The financing of such positions will continue to rely on a mixed source of funding, incl. external grants and various categories of faculty funding such as (in Swedish) GRU, Verksamhetsbas-stöd, FAKIR, included in the annual Rector Contracts (Rector Contract). The introduction of a new and separate Doctoral Programme in Theoretical Chemistry and Biology is in line with the strive of the BIO school to more clearly visualize its research activities to the society (BIO school Strategy Plan 2009-2012).

APPENDIX 1: Study Plan for the Research Education Subject "Theoretical Chemistry and Biology"

DOCTORAL PROGRAMME IN THEORETICAL

CHEMISTRY AND BIOLOGY

APPENDIX 1

Study Plan for the Research Education Subject

Theoretical Chemistry and Biology


Study Plan for the Research Education Subject "Theoretical Chemistry and Biology"

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Table of contents

Section Page

1. Subject description and goal for the education 3 2. Research topics 4 3. Structure of the education 4 4. Obligatory and recommended courses 5 5. Thesis 7 6. Eligibility and selection 8 7. Examina and tests in the education 9


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tudy plan for the research education subject Theoretical Chemistry and Biology, at the KTH School of Bioptechnology. Common regulations and guidelines for research education studies at KTH are available in the university´s central regulations

collection "KTH handbook: Regulations for education at research level". The present study plan for education at research level in the subject Theoretical Chemistry and Biology shall be seen as a complement to the common regulations by the following subject specific specifications.

1. Subject description and goal for the education

1.1 Scientific field

Theoretical Chemistry and Biology is an interdisciplinary scientific field where physics theory, mathemathics and computational science is used to investigate, explain and predict chemical and biological phenomena and processes, including material properties.

1.2 Overall goals for the education

The overall goals of the Doctoral Programme complies with the goals for the research education that have been layed down by the faculty of KTH: The aim is to provide the society with researchers who can contribute to the development of a sustainable society. The research students shall become independent and excellent researchers. After completed studies the research student in the Doctoral Programme in Theoretical Chemistry and Biology shall be able to:

• Describe and explain theories and empirical results within the area of specialization • Formulate concrete research questions within the area of specialization • Use scientific methods and develop new knowledge through own scientific studies • Critically analyze and evaluate used methods and results from own and others scientific studies • Present and discuss research results within the scientific community • Present research in a pedagogical manner outside the scientific community and in educational situations • Valuate ethical aspects concerning research within the area of specialization and being able to act accordingly

S


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• Identify needs for new knowledge and have the ability and knowledge to initiate and lead research activities

Beyond these overall góals, there are specific goals for this research education subject. In particular, after completing the education, the student should: Knowledge and understanding

• Have a broad, scientific foundation to be able to work within the areas of theoretical chemistry and biology, or general mathematical modelling. This knowledge should include basic programming skills, knowledge of basic numerical mathematical methods, and various applications to chemical or biological problems.

• Show broad knowledge within the area, including knowledge in computer modelling and natural science, and essentially deepened knowledge within certain parts of the area.

Skills and abilities

• Show a good ability to, independently as well as in a group, be able to apply knowledge and abilities in practical activities with regards to relevant scientific professional and social judgements and viewpoints.

• Show a good ability to analyse, formulate, and handle problems from a research-oriented perspective, being able to define clear scientific questions, design a strategy for solving the problem at hand, and possess the necessary skills to solve research problems in theoretical chemistry and biology.

• Possess individual and professional skills like languages, leadership, project management, and communication for work as a researcher in a research-oriented company, a research leader in a technical intensive company, or in order to be able to continue toward a research career.

Judgement and Approach

• Have very good understanding that research-related problems are often complex, can be incompletely defined and sometimes contain conflicting goals and conditions.

• Be aware of the responsibility and the ethical viewpoints which can arise in connection with different technical, organisational, economical, ecological and social activities.

2. Research topics Theoretical Chemistry and Biology, highlighting basic concepts and methods as well as important application areas, like chemical catalysis for sustainable energy, atmospheric chemistry, nanobiotechnology, enzyme catalysis, drug design, biomolecular visualization and engineering, protein dynamics and properties of modern “soft” matrials in general. 3. Structure of the education The education in Theoretical Chemistry and Biology at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the subject of Theoretical Chemistry and Biology. Courses can be arranged by the home university, or other national or international universities, institutes or companies. Note that


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the quality and level of courses arranged by others than university bodies need to be approved by the director of post-graduate studies before these can be part of an individual course package. In case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be defended at a dissertation at the end of the studies (see section 5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 4. Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponidng to two years of full-time studies). At least 50 % of the course credits (=15 ECTS) should correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponidng to four years of full-time studies). At least 60 % of the course credits (=36 ECTS) should correspond to courses at research level. L= Obligatory for licentiate degree exam D= Obligatory for doctoral degree exam Advanced Courses

Code

Name of course

Credits (ECTS)

THEO CHEM AND BIOL

NM: MC3 Mathematical and Numerical Methods for Chemists and Biologists

10 R

FBB3030 Computational Chemistry 8 O (L/D)

FBB3060 Molecular Modelling, Basic Applications 8 O (L/D)

FBB3050 Thermodynamics and Statistical Mechanics 10 O (D) NM:OC9 Catalysis 5 R BB3060 Protein Physics 5 R FBB3060 Molecular Dynamics and Monte Carlo Techniques 7.5 R F£A5708 Computational Enzymologi 5 R NM:OC10 Multiscale Modelling 10 R NM:OC8 Computational nano and bionano technology 10 R DD2397 Bioinformatics 7.5 R KJE-3104 Relativistic Quantum Chemistry 10 R NM:OC6 Molecular Properties 8 R XXX Protein (biomolecular) visualization and haptics 5 R 26.0 ECTS

as O


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Research Skill Courses

Code

Name of course

Credits (ECTS)

THEO CHEM AND BIOL

BB3110 Scripting 5 R 1N5113 Theory of Sciece and Research Method,

Technological and Natural Sciences 7.5 O (L/D)

Conditional TBD Elements of Scientific computing 5 R ME2016 Industrial Project Management 4 R

7.5 ECTS

as O

Broadening Courses

Code

Name of course, (level)

Credits (ECTS)

THEO CHEM AND BIOL

DD2435 Neural Networks 7.5 R DD2398 Quantative System Biology 3.0 R TBD Protein visualization and haptics 3.0 R 2E1395 Pattern recognition 4 R 0.0 ECTS

as O Other Courses

Code

Name of course, level

Credits (ECTS)

THEO CHEM AND BIOL

LH200V Basic communication and teaching (GKU) 3.0 O (L/D) Conditional

BB3120 Handledningsmetodik flör projektarbete (R) 6.0 R 3.0 ECTS

as O Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligibile for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved. Further, in order to be able to fully benefit from the research studies in the subject Theoretical Chemsitry and Biology it is beneficial for the students to have aquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH:

- DD1352: Algoritmer, Datastrukturer och Komplexitet - EL1820 Modellering av dynamiska system - MC1 (Masters CCP): Quantum chemistry and physics - MC2 (Masters CPP): Chemical Kinetics and Dynamics - MC3 (Masters CCP): Mathematical and Numerical Methods for Chemists


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- MC4 (Masters CCP) : Scientific programming - DD2398 Kvantitativ systembiologi - SG1216 : Termodynamik

These so called special admission requirements concerning courses or oher qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 5. Thesis The thesis part is an obligatory part of the research education. In addition the the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),

the following criteria, representing the present praxis and norm for the scientific field, should serve as guidelines related to the content and quality of doctoral and licentiate theses. Cases for which these guidelines for any reason are not considered applicable or relevant should be discussed with the Director of post-graduate studies and the Dean of KTH-School of Biotechnology.

- DOCTORAL THESIS -

Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on four papers. • Normally, two of the included papers should either be already published or formally

accepted for publication ("in press") in international peer-reviewed scientific journals. Additional papers could be included as manuscripts, preferably as "submitted for publication" to international peer-reviewed scientific journals.

• The student should appear as first author on at least two of the papers, including one of the papers belonging to the "published or in press" category.

• For any paper included, his/her contribution should be significant and clearly identifiable. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also

by at least one senior scientist.

• In case a thesis is based solely on manuscripts which are not already published or formally accepted for publication ("in press") in international peer-reviewed scientific journals, the thesis and the manuscripts should be pre-examined prior to printing, in addition to the main supervisor and at least one senior scientist also by the faculty opponent and the evaluation committee.


should be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also

by at least two senior scientists and the Director of post-graduate studies.

- LICENTIATE THESIS -


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Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on two papers. • The included papers need not to be already published or formally accepted for publication

("in press") in peer-reviewed international scientific journals. However, at least one manuscript should normally be included as "submitted for publication" to an international peer-reviewed scientific journal.

• The student should appear as first author on at least one of the papers included. • For any paper included, his/her contribution should be significant and clearly identifiable. • If the thesis includes one or more paper which are published or formally accepted for

publication ("in press") in an international peer-reviewed scientific journal, the thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least one senior scientist.

• If the thesis does not include any paper which is published or formally accepted for publication ("in press") in an international peer-reviewed scientific journal, the thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least two senior scientists.


should be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also

by at least two senior scientists and the Director of post-graduate studies.

6. Eligibility and selection

Basic and special eligibility and prior knowledge

Eligibility to the Doctoral Programme in Theoretical Chemistry and Biology first involves the basic requirements for admission to research studies in general set forth by the Swedish Government (see "Högskoleförordningen", chapter 7, §39):

1. a completed university exam at advanced level, 2. fullfilled course requirements of at least 240 ECTS, of which at least 60 ECTS is at advanced level, or 3. corresponding merits acquired through other procedures

Further, for admission to the Doctoral Programme in Theoretical Chemistry and Biology, the completed university exam or the advanced level courses should be in a relevantsubject area. In addition to these requirements, also special requirements for a particular area may apply. These are in such cases described in the section "Crediting of earlier taken courses". When included, these requirements are deemed necessary for the students to profit from the training, and may for example involve knowledge/skills from university studies in particular areas of importance for the subject area or language skills. The requirements are the same for students aiming for either doctoral or licentiate degrees.


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Selection criteria

The selection of students to research education is first based on that they formally fulfill the admission criteria. In addition, their ability to fully benefit from the research education is assessed during the admission process, typically through interviews and reviewing earlier activities, exams and records, but also through an evaluation of the talent, degree of maturity, independency, expression ability in writing and speech, language skills and ability of critical thinking. The selection is done by the Dean of the School of Biotechnology after assessment o

f the appointed main supervisor and co-supervisor(s) by the Director of postgraduate studies.

7. Examina and tests in the education

Licentiat and doctoral exams Licentiate and doctoral degree exams are performed according to the KTH regulations (see "KTH-handboken" at http//:intra.kth.se). A licentiat degree exam may be a final exam. Even if a doctoral exam is the final exam, a licentiat degree exam may first be taken. Briefly, in addition to completion of full course packages of 30 or 60 ECTS, for licentiate and doctoral degree exams, respectively, both exams involve a defence of a thesis as a result of theoretical and/or practical investigations. A licentiate thesis is presented at a public seminar. The licentiate thesis shall be examined by at least one lecturer/senior scientist. The main supervisor decides on pass or not. A doctoral thesis exam involves a public defence seminar at which the thesis is examined by an opponent and an evaluation committe consisting of three or five members, the latter deciding on approval of the thesis or not. Tests that are included in the education Courses in the research education shall preferably involve either an oral or written examination. The examinor must in each individual case ascertain that the student has fullfilled the course requirements.

APPENDIX 2: Listing of supervisor capacity

DOCTORAL PROGRAMME IN THEORETICAL CHEMISTRY AND BIOLOGY

APPENDIX 2

Listing of supervisor capacity

At present four professors, two guest professors and three associate professors/senior lecturers (w. PhD exams) are active within the proposed Doctoral Programme. Also, a new senior lecturer (w. PhD exam) position is presently being appointed. Three professors at other KTH departments will particpate in the program. Thus, in total, 13 senior scientists (ten at the School of Biotechnology) will be able to operatively act as main supervisors in the Doctoral Programme of Theoretical Chemistry and Biology. In addition, other senior scientists active at the Division of Theoretical Chemistry and Biology within the School of Biotechnology, are likely to be promoted to associate professors within 5-10 years, and thus can act as main supervisors for licentiate or PhD students within the Doctoral Programme.

PRIMARY AREAS OF EXPERTISE

PH

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Professors Hans Ågren • • • • • Faris Gelmukhanov • • • • Yi Luo • • • • Kersti Hermansson • • • Boris Minaev • • • Chuankui Wang • • Erik Lindahl • • • Erik Aurell • • Aatto Laaksonen • • • • Associate Professors

APPENDIX 2: Listing of supervisor capacity

Olav Vahtras • • • Ying Fu •

• • •

Yaoquan Tu • • • •

Zilvinas Rinkevicius • • • • Doctors/Senior scientists

Mårten Ahlquist • •

Yun Chen • •

APPENDIX 3: Course list

DOCTORAL PROGRAMME IN THEORETICAL CHEMISTRY AND BIOLOGY

APPENDIX 3

Course list Obligatory (O) and recommended (R) courses for the research education subject Theoretical Chemistry and Biology within the Doctoral Programme of Theoretical Chemistry and Biology. The courses are divided into the four categories (A) Advanced courses, (B) Research skill courses, (C) Broadening courses, and (D) Other courses. Advanced Courses

Code

Name of course

Credits (ECTS)

THEO CHEM AND BIOL

NM: MC3 Mathematical and Numerical Methods for Chemists and Biologists

10 R

FBB3030 Computational Chemistry 8 O FBB3060 Molecular Modelling, Basic Applications 8 O FBB3050 Thermodynamics and Statistical Mechanics 10 O NM:OC9 Catalysis 5 R BB3060 Protein Physics 5 R FBB3060 Molecular Dynamics and Monte Carlo Techniques 7.5 R F£A5708 Computational Enzymologi 5 R NM:OC10 Multiscale Modelling 10 R NM:OC8 Computational nano and bionano technology 10 R DD2397 Bioinformatics 7.5 R KJE-3104 Relativistic Quantum Chemistry 10 R NM:OC6 Molecular Properties 8 R XXX Protein (biomolecular) visualization and haptics 5 R 26.0 ECTS

as O For licentiate and doctoral degree students within the research subject, the two courses "BB3030 Computational Chemistry (8.0 ECTS)" and "BB3060 Molecular Modelling, Basic Applications (8.0 ECTS)" are obligatory. For doctoral degree degree students within the research subject, the course “FBB3050 Thermodynamics and Statistical Mechanics” is obigatory in addition. Research Skill Courses

Code

Name of course

Credits (ECTS)

THEO CHEM AND BIOL

BB3110 Scripting 5 R 1N5113 Theory of Science and Research Method, 7.5 O


Technological and Natural Sciences

TBD Elements of Scientific computing 5 R ME2016 Industrial Project Management 4 R

7.5 ECTS

as O If not already taken before admission to research studies (for example the KTH D-level course "AK2036 Scientific Theory and Research Methodology (7.5 ECTS)", obligatory for students in several KTH Masters programs, a course in research methodology is conditionally obligatory for all students of the Doctoral Programme. The KTH course "1N5113 Theory of Science and Research Method, Technological and Natural Sciences (7.5 ECTS)" is listed here as a course on this theme, but this particular course may be exchanged for an equivalent one.

Broadening Courses

Code

Name of course, (level)

Credits (ECTS)

THEO CHEM AND BIOL

DD2435 Neural Networks 7.5 R DD2398 Quantative System Biology 3.0 R TBD Protein visualization and haptics 3.0 R 2E1395 Pattern recognition 4 R 0.0 ECTS

as O

These courses are to be annually arranged literature seminar courses, in which research topics of general and broad interest are presented and discussed. The courses serve as an important forum for cross-disciplinary interactions, scientific and social networking and competence broadening. For both doctoral and licentiate degree students, it is obligatory to participate in at least one round of this seminar series.

Other Courses

Code

Name of course, level

Credits (ECTS)

THEO CHEM AND BIOL

LH200V Basic communication and teaching (GKU) 3.0 O BB3120 Handledningsmetodik flör projektarbete (R) 6.0 R 3.0 ECTS

as O

The course "LHV200V Basic Communication and Teaching (3.0 ECTS)" is obligatory for research students in the Doctroal Programme which will act as teachers or laboratory assistants during their research studies. It is thus considered conditionally obligatory for the Doctoral Programme in Theoretical Chemistry and Biology.

Summary of obligatory and conditionally course credits for the research education subject

Licentiate degree Doctoral Degree Obligatory 16 26

Conditionally 10.5 10.5


Obligatory

Total

26.5 ECTS

36.5 ECTS

The span 16.0 - 21.5 ECTS corresponds to 53 - 71 % of the 30 ECTS of course credits required for a licentiate degree exam. The span 26.0 - 36.5 ECTS corresponds to 45 - 60 % of the 60 ECTS of course credits required for a doctoral degree exam.

APPENDIX 4: Listing of national and international networks

DOCTORAL PROGRAMME IN THEORETICAL CHEMISTRY

AND BIOLOGY

APPENDIX 4

Listing of national and international networks related to the doctoral programme in Theoretical Chemistry and Biology (as of autumn 2010)

Name Type of

network Host /Coord,

Body Main Financial

Support Approx. duration

KTH-USTC China center in Bio and Nano Materials

PhD student and science exchange

KTH, USTC China - MOST, CAS

2015

KTH-CSC Student Exchange Programme

KTH Cina - CSC -

CCMSB – Center of Computatonal Molecular and System Biology

Center for Education (Masters programme, Doctoral Courses)

KTH and SU KTH and SU 2010

KTH-IACS-PKU Trilalateal center

Stduent Exchange KTH, IACS (Kolkatta), PKU (Beijing)

KTH, IACS, PKU 2013

EUROINDIA Erasmus Mundus Student Exchange Programme

KTH EU 2012

MONAMI EU Cooperation Network

UU EU FP7 2013

SCALALIFE EU CapacityNetwork KTH EU FP7 2014 HIPERSOL EU Cooperation

Network Barcelona EU FP7 2013

CODECS EU COST Network CNR - Pisa EU COST 2014 NORCAPP Nordic Network of

Centers of Excellence Tromsoe Univ.

Nordic Council of Ministers

2012

X-ray-DNA STINT (Japan) KTH STINT 2012 Mol-MAGN VR/SIDA KTH VR 2011 Photo-LED SI/Visby KTH SI 2011 Nano-PV KTH-UU (STANDUP)

research center for 3rd generation solar cells

KTH Government/ EIT 2015

application for a/teoretisk kemi och... · application for a doctoral programme in theoretical...

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