PhD Course

PhD and graduate course: Science and technology of self-replicating systems and unconventional computing

Description
This course provides an introduction to the physics, (bio)chemistry and computational science of self-replicating systems. It is designed for PhD students and advanced MS students e.g. from physics, chemistry, nanobioscience, synthetic biology, molecular biology, pharmacy, robotics as well as computer, electrical and mechanical engineering.

The course consists of hands-on:

  • chemistry labs (assembly and characterization of simple protocell components),
  • electronics, software and mechanics workshop (3D printer assembly)
  • computer simulations (molecular aggregate simulations and evolutionary experimental planning using machine learning)
  • tutorials (lectures) on theory and methods for involved key issues.

Besides providing the necessary introductions to the basic science, the course also introduces the students to do-it-yourself (DIY) open source hardware.

The course concludes with a discussion of case studies on how to write scientific grant applications as well as how to address the press and the general public regarding complex scientific issues (and how these two issues are connected).

Since some of the teachers also have their own businesses within this rapidly growing area, this PhD course may also be of interest for potential entrepreneurs.

Course Credit

  • 5 ECTS, needs to be approved at the students home institutions and the estimatedtime and effort is 125-150 hours, with about 45 hours of lectures and labs.
  • Minimum attendance of 5 out of 6 days of the course.
  • Mandatory participation in the public outreach event.
  • In order to get credits for the course, every student has to be present at all the other students’ talks.

 

Evaluation

(Exam) evaluation is pass / non-pass and it consists of three parts:

(i)

  • Active participating in the six course days. The last days of the course, students give a ten minutes presentation (a few slides) that suggests how the concepts and methods encompassed in this course could be a valuable inclusion in the project they are already involved in (personal / Ph.D. project). After each presentation a short discussion with questions and suggestion follows. All participants have to be present during the presentations and actively participate in the discussions.

(ii)

  • Oral examination on elected topic (~ 30 mins), final date to be determined.For the evaluation the participants have to choose between two types of oral presentations:

The participant gives a 15-20 minutes presentation about a topic or technique related to the course curriculum (e.g. a paper). Importantly, the presentation should not be related to the student's own PhD project.

  • Participants team up in groups of two persons and give a presentation on a hypothetical project/paper that combines the competences that each student has. The students should not already be working on closely related projects in the same group. Ideas for projects could e.g. come from the student presentation day. (Each student from the two person team does the oral examination separately).

(iii)

  • Short public presentation: A short talk (5-10 mins, TED style presentation) on a your PhD (or related) topic where you frame your work in a larger scientific picture, in societal issues and if it makes sense how it relates to the overarching course theme. This short talk will be part of a larger public event on unconventional computing and self-replicating systems.

Dates and venue

March 2-7, 2015, lectures and labs, University of Southern Denmark,

April 22, 2015 , oral exam, University of Southern Denmark,

April 23, 2015 , short public lecture in Odense and/or Copenhagen, times and location(s) to be determined.

Registration

Send email to all organizers (see below) with your student status and area of expertise.  Please sign up as soon as possible, and no later than February 15, 2015, as we need to order 3D printer kits to participants (no charge to students) and plan the labs.


Organizers

Steen Rasmussen, FLinT, steen@sdu.dk, +45-6011-2507, main coordinator.

Aleksandra Amaladass, FLinT, alama13@student.sdu.dk, +45-5018-0038

Lene Andersen, FLinT, lenea@sdu.dk, outreach planning.

 

Teachers include

Steen Rasmussen, University of Southern Denmark & Santa Fe Institute, USA

Pierre-Alain Monnard, University of Southern DenmarkCarsten Svaneborg, University of Southern Denmark

Norman Packard, ProtoLife Inc., USA & Ca’Foscari University, Italy

Masayuki Imai, Sendai University, Japan

Clements Yanev, Future Bits Open-Tech UG, Germany


Venue

Center for  Fundamental Living Technology (FLinT), Department for Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark http://flint.sdu.dk, +45-6550-2507 lab / 4436 sec

Cost

The course is free of charge for the registered and accepted students. Expenses for the experimental labs as well as the 3D printer are paid by the course. Thus, the students may bring their 3D printer home after completion of the course. Accommodation and travel costs are expected paid by the students (or their home institutions).

Detailed (tentative ) schedule:

Monday, March 2, 2015
10:00-10:15  Welcome and introduction to the course on self-replicating systems and unconventional computingSteen Rasmussen, University of Southern Denmark & Santa Fe Institute, USA
10:15-12:15  Minimal living and intelligent processes: self-replicating protocells, self-replicating machines printers, machine learning and personal fabricators Steen Rasmussen, University of Southern Denmark & Santa Fe Institute, USA. 
12:00-13:00 Lunch
13:00-15:00 Soft-matter physics and protocells: experimental and theoretical tutorialMasayuki Imai, Sendai University, Japan
15:00-17:00 Biochemistry of protocells, tutorial of experimental bottom up & top down approaches Pierre-Alain Monnard, University of Southern Denmark

Tuesday, March 3, 2015
8:00 – 17:00 Hands-on laboratory on the assembly and characterization of fatty acid vesicles, investigation of droplet motility and division, minimal metabolic reactions (details depend on number of course participants)Pierre-Alain Monnard, Masayuki Imai & Steen Rasmussen 

Wednesday, March 4, 2015
9:00-10:30 Introduction to computer simulation of mesoscopic molecular aggregates, Carsten Svaneborg, University of Southern Denmark 
10:30-12:00 Hands-on computer simulation labs
12:00-13:00 Lunch
13:00-14:30 Evolutionary search and experimental planning Norman Packard, ProtoLife Inc., USA & Ca’Foscari University, Italy
14:30-17:00 Hands-on computer demonstrations of evolutionary search and continuation of molecular simulations from the morning. Carsten Svaneborg & Norman Packard

Thursday, March 5, 2015
8:00 -17:00 Assembly of your own 3D printer, hands-on (limited to 10 (ten) 3D printers) Clements Yanev, Futute Bits, Open-Tech UG, Germany

Friday, March 6, 2015
8:00 – 17:00 Assembly of your own 3D printer, hands-on activities (limited to 10 participants)Clements Yanev, Future Bits Open-Tech UG, Germany

Saturday, March 7, 2015
9:00-10:00 Different funding agencies, case studies on grant writing, application composition: scientific content, technological impact and societal narratives. Steen Rasmussen, University of Southern Denmark & Santa Fe Institute, USA
10:00-11:00 Addressing the press, the general public and the composition of short public lectures on (complex) scientific issuesSteen Rasmussen, University of Southern Denmark & Santa Fe Institute, USA
11:00-12:00 Student presentations (ten minutes and a few slides) that suggest how the concepts and methods encompassed in this course could be a valuable inclusion in the project they are already involved in (personal / Ph.D. project). After each presentation a short discussion with questions and suggestion follows.
12:00-13:00 Lunch.
13:00-14:00 Student presentations continued. 
14:00-16:00 Student teamwork on preparation for oral exam and short public lecture, which is scheduled approximately a month and a half later, April 22 and 23, 2015 .  
16:00 Departure