Acknowledgments

This thesis could not have been written without the support of many people. More than just scientific support I received lots of emotional support which is essential yet underrated. To express my gratitude for this support I want to acknowledge the wonderful people who made this possible.

First, Pieter Rein, thank you for sticking with me, having my back, fighting for me, and helping me through thick and thin. You always were able to reignite my enthusiasm, even when my own motivation would waver. You provide a great atmosphere for research, you are always available for discussions, you care about the people at least as much as about the project, and you are willing to consider different perspectives and evolve your views. Your commitment to fair, open, and rigorous science is one of your strongest qualities. During our many meetings I learned a lot from you, not just about research but more generally about life.

Thank you also to my co-supervisor Gašper. Your advice can only be described as magical. Many times, when Pieter Rein and I found ourselves stuck on a certain problem, an email to you would result in an eager reply filled with extremely useful suggestions and creative ideas that set us back on track. I also deeply appreciated your hospitality when you hosted me in Vienna for a few weeks; I felt warmly welcomed by your group and left truly inspired.

Mareike, you were the first person I met when I stepped into AMOLF on my first day as a master’s student. I immediately sensed a connection with you. My senses did not betray me; from that moment on we started developing a friendship that has become one of my most treasured. You have been of tremendous importance to me, and I am not exaggerating when I say that without you, this thesis would not exist. It all started even before I moved to Amsterdam. As a master’s student contemplating an internship position at the biochemical networks group at AMOLF, I looked for the most recently hired PhD student in this group—you—and emailed to ask about the work environment. The response I received was not only overwhelmingly positive but also incredibly kind, convincing me to come to Amsterdam. About a year later, when I was offered a PhD position at AMOLF, you were the first person I wanted to share the news with. I vividly remember our joy about me being able to stay for 4 more years. Throughout the ensuing PhD time, your example and enthusiasm provided strong guidance and support. But you have been far more than a wonderful mentor at AMOLF. Many of our cherished stories unfolded outside of work, including countless trips, crazy parties and beautiful evenings sharing a bottle of wine. Many of the people that I thank below I know through you. I am happy to look back and see that we built a little community here in Amsterdam that has shaped our lives. I feel so grateful for having met you.

I want to thank my paranymphs, Christian and Katharina, who have been a never-ending source of inspiration, support, and fun over the course of my PhD. Chris, I am deeply grateful for the privilege of closely sharing the journey of life with you over the past few years. Our friendship means so much to me. You genuinely care about the people close to you, and your presence is a gift. Maybe you don’t know this but I admire your eloquence. You have a remarkable ability to find words for expressing your sensations and feelings genuinely and precisely. With this comes a deep sense of security that you embody and radiate. With you by my side I feel empowered to push boundaries and step out of my comfort zone, yet always feeling safe. I look back on so many joyful, exciting, and daring adventures we shared and undoubtedly will keep sharing. It is rare to find someone like you whom I can fully trust one hundred percent. Moreover, your enthusiasm is contagious and when you deeply care about something it is truly inspiring and moving. We have transformed together, learned so much through each other, and I am certain that our mutual growth will continue. Kathi, you are a beacon of joy in my life. Over the years, we must have accumulated hundreds of hours of talking to each other about anything and everything. I remember countless times of coming to your office or to the tweezer lab for a “quick question” or a bit of gossip, only to find ourselves, two hours later, still completely lost in conversation. With you, any ordinary activity transforms into an exciting mission, whether it’s shopping for lamps, finding the best Airbnb, shooting a movie scene, exploring activities at Christmas lunch, or discovering the best party locations at pride. We complement each other so well as a team and I am looking forward to our future missions. You care deeply about the people around you, always willing to help with a lot of empathy. Because you’re naturally drawn to reflect deeply on situations and people, your advice is incredibly valuable and thoughtful. I know that whenever I struggle, I can count on you. Moreover, I admire your devotion and energy for pursuing the things you care about, whether it is a scientific publication, sleeping for a night in the mad king’s castle, fairly managing interpersonal conflict, or obtaining K-pop tickets for a sold-out show. Thank you for all the time we spend together—whether dancing, supporting each other, deeply reflecting about philosophy, working on a project, or simply being in each other’s presence.

Next, I want to thank my partynymphs, Lucie and Imme, for bringing so much light and enlightenment into my life. Imme, we met during a global pandemic, yet we managed to build a close friendship within weeks. And then you had the wonderfully bold idea of doing a house swap: me living in Utrecht and you living in Amsterdam for a week. It was a success and your house since has always felt like a second home to me, a special and beautiful connection. I am happy to say that bold ideas and outside-of-the-box thinking are rather the rule than the exception with you. You are so inspiring! You introduced me to the wonderful sport of ice skating, which I started enjoying so much that we decided to sign up for courses together religiously every winter. You also made me listen to your favorite Dutch artists which led to me enjoying the music so much that we ended up going to music festivals together for it. I am curious what will come next! We have navigated ups and downs together, forging a bond so strong that I am convinced we will remain connected, no matter what the future holds. Lucie, with our overlapping social circles, it was only a matter of time before we became friends ourselves. Yet, when our friendship finally formed, it surpassed all my expectations. We have incredibly deep chats about a plethora of topics, and I am very grateful for all the amazing advice you offer. Not only that, but we can also laugh endlessly over the same »joke« for months. You are so much fun to be around! And your heart is in the right place, too. Your passion for fighting patriarchy and tackling the climate catastrophe is powerful and contagious. The energy and thought you bring into your relationships—with your partner, family, friends, and yourself—deeply inspire me. Thank you for sharing your enthusiasm and opinions, your joy and wisdom.

Laura, meeting you led to the single most impactful shift in my Amsterdam life. Without knowing each other all too well, we decided not only to move in together, but also to plan a holiday to Belice. Although we ended up going to Mexico instead, I am glad that we took the courage for both decisions as they marked the start of our adventures together. You are a wonderfully kind and loving flatmate, as well as a brave and enthusiastic travel companion; what a unique combination! Beyond Mexico, we have explored many beautiful locations together, including Noordwijk, Vienna, Nice, Munich, and Colombia. I hope this is only the beginning of a list that will keep growing. Not only that, but we also manage to make life in Amsterdam an adventure. We have seen countless movies together, shopped in the most exclusive boutiques, we have been partners in crime (literally). Our shared excitement for niche French concerts brings me joy. I also want to especially thank you for supporting me in the final and sometimes challenging stretches of the PhD. You made that time so much easier for me. With few people can I feel such uninhibited joy as with you and I want to thank you for that.

I want to thank my present and past colleagues from the biochemical networks group for making daily work so enjoyable. To Harmen, who left the group not long after I started, thank you for welcoming me into the group and helping me get started. Alex, I remember many fun lunches with you and Mareike during the pandemic which would represent the highlight of my day. You have a great sense of humor as well as very deep knowledge about many topics but what stands out most about you is your sense of true curiosity. Not only are you curious in a scientific sense about the mysteries of the world, but even more so curious and enthusiastic about the people that surround you. Thank you for our deep conversations, for your advice and wisdom. Age, we started our PhD on the same day, and our defenses are only six days apart. It has been such a joy to embark on this journey alongside you. I admire your capacity for structured thought, your analytical math skills and your pragmatic, down-to-earth attitude. It makes working with you a real inspiration and joy. I feel we are such a good team together, which is proven by how quickly we were able to finish our project together. I enjoyed all the conferences that we went to together. I also appreciate your sailing skills that saved us from the sand bank. Jenny, thank you for radiating joy and excitement as well as always being willing to engage in thoughtful debate about topics that you care about. Mike, I greatly appreciated your passion for helping everyone in the group with our projects. Your vast knowledge and willingness to share it truly made a difference. Muriël, it was a pleasure to supervise you and witness you gradually taking ownership and responsibility for your project. Maxim, your good spirits and intelligent questions were consistently inspiring and your project became a big success. Ramon, I’ve had some of the most interesting conversations with you; thank you for sharing your knowledge. I applaud your principled attitude towards science and societal topics in general; you represent integrity and honesty in a way few people do. I thank you for your involvement in the works council for improving working conditions for everyone. Avishek, I am happy that after getting acquainted with each others’ humor, we can finally laugh so much together. I deeply appreciate all the work and thought you put into extending PWS and all the incredibly illuminating discussions we had as a result. Julien, though I often only saw you on screen during group meetings, your visits to Amsterdam were always a lot of fun. I especially fondly remember cooking a delicious meal with you on the sailing boat during our group outing. Vahe, I appreciate your unique perspective on science and your genuine fascination for nature and physics. Daan, I am delighted by your unconventional way of thinking, which adds so much value to the group! Thank you for bringing Dutch poetry to the group lunch. I wish you a lot of success in finishing your PhD. Claudio, you radiate positive energy. In the relatively short time you have been at AMOLF, we have connected on so many layers beyond science. Menno, you just started your PhD and even though we overlapped very briefly, I enjoyed exchanging ideas with you. Geert and Robin, it was a joy to see you taking on your master’s projects with enthusiasm and finishing them successfully.

Bela, thank you for showing up for the daily coffee break, every morning at 10:30, without fail. Fortunately, even during the pandemic you insisted on keeping the coffee break alive via virtual sessions, which I am very grateful for. I don’t know how I would have been able to endure the social isolation without these regular meetings. Both the virtual and the real coffee breaks were essential for creating a feeling of connection and belonging within the group. Your retirement from AMOLF had a big impact on me and the group, and coffee breaks would not be the same anymore but I am happy that you are still regularly coming to AMOLF even after your retirement.

A special thanks goes to our experimental collaborators at AMOLF. Fotis, your expertise of E. coli chemotaxis is spectacular and talking to you about the biological intricacies was very fascinating and useful. Evan, I admire your determination and attention to detail in doing complex single-cell E. coli experiments. Moreover, your way of presenting science is magnetic. Thank you for putting your heart into this project! Tom, thank you for seemingly never stopping to think deeply about any research question as well as for all the advice you have offered me. Your scientific questions and comments show a very deep understanding of and passion for science. Your interest in my projects was always a huge motivator.

I also enjoyed fruitful collaborations and interactions beyond AMOLF. A special thanks goes to my collaborators at MPI-CBG in Dresden. Anne, you took the initiative in forming a collaboration between our labs and I am so grateful for that. It was amazing to see how you managed to build the mathematical tools to answer a question that seemed so difficult to address. I enjoyed working with you and talking with you. With you, it’s a double-edged sword. One one hand, I am excited to have found someone that works in the same niche as me. On the other hand, you also humble me as you clearly understand information transmission on deeper level than me. Christoph, thank you for many insightful conversations and your honest feedback on ideas and drafts.

A special thanks also goes to the members of the Tkačik lab at ISTA who welcomed me so enthusiastically during my time in Vienna. Camila, Tereza, Natalia, Bahti, Julian, Athina, Simon, Réka, Michal, David, it was great meeting all of you. I particularly enjoyed our stimulating conversations about science and many other topics in the cafeteria as well as various fun trips into the city of Vienna.

Beyond those I directly worked with, I want to thank many other people at AMOLF whom I am very grateful to have gotten to know during my PhD. Moritz thank you for your kindness, loyalty, and for being a fantastic companion in our bouldering sessions and as we learned to climb outdoors together. Anne-Sophie, it is always so much fun (and perhaps slightly unproductive) when we are in the office together. Thank you for all the hilarious, deep, senseless, and funny conversation. Moreover, I want to thank you for all the absurd adventures we have had together outside of work. Every memory we make is a great one and we are unquestionably gifted at picking out amazing locations to eat or to party. I look forward to our future adventures! Kim, thanks for sharing your incredibly positive energy. The year you were at AMOLF was so much fun. Francesca it is always fun to go bouldering together and I enjoyed the parties together. Thank you for bringing me into your friend group. Timo, thank you for sharing your passion for cooking and preparing some chef-quality meals and desserts. You are incredibly generous. Lori, it was fun to chat and play board games with you. I enjoyed being your neighbor.

I want to thank the PV, the staff association which brings so much energy and fun to AMOLF through its events. Thanks to Jente, Yvonne, Evelijn, Igor, Sofija, Mels, Mees, Teressa and all the other PV members, past and present. I deeply appreciate your efforts to bring joy to the AMOLF community, and I cherish the years I spent in the PV myself. Especially the Christmas party was always such a blast!

A very big thank you to the support departments of AMOLF. In particular, I want to thank for the great support from the ICT department in setting up and maintaining the computational cluster which was indispensable for me. Thanks, Gerben, Michiel, Sean, Kallinikos, Cees, and Pieter for solving all the problems regarding the cluster. I appreciate all the work that goes into maintaining it working. Thanks also Erny and Petra for helping with communicating my research to a wider audience and for organizing the Science Day. Thanks to Clyde for caring about workplace ergonomics, to Hinco for being able to fix anything, anytime and being cheerful meanwhile. I appreciate the HR department, especially Wouter and Linda, for helping me find housing and answer all contract-related questions.

I also want to thank the wonderful people I met outside of AMOLF and that shaped my life. Nina, thanks for the joy of dancing together, for chatting endlessly, and for sharing our passion for music. Maxime, thank you for bringing so much fun, for patiently teaching countless board games, and for the wonderful time you spent in Amsterdam; it was truly a joy having you here. Victor, every time I see you you cheer me up with your humor and positive attitude. Thank you for taking me to the best Mexican concert in Amsterdam. Lucas, your friendly calmness is addictive. You’ve got a great sense of humor and I admire your dedication to finishing what you started, whether it is a bike race or a very hot chili pepper. Mirko, you are wonderfully down-to-earth and have a perfect subtle wit that always makes me laugh. Tamara, you are a person full of life and love. Thank you so much for sharing your amazing joy with the people around you.

And, thank you to my friends from back home in Germany. Victoria, thank you for always being on my side. Dennis and Lukas, you both know me since the very early days. It makes me so happy that we still maintain a connection that persists through all the changes that life brings. I am so curious where all our journeys will bring us. Ben, Stefan, Flo, Julian, Veronica, Rudi, Christian, thanks for helping me with the physics homework during our studies. The effort finally paid off. We have all come such a long way since then!

Finalmente, gracias a mi familia. Vuestro amor incondicional ha sido tan importante para mí. Gracias por celebrar cada logro conmigo y por ayudarme en los momentos difíciles. Mamá, gracias por estar siempre a mi lado y ayudarme en todas las situaciones y etapas de mi vida. Gracias por dejarme la libertad de hacer lo que a mí me gusta y encontrar mi propio camino. Gracias por leer conmigo y enseñarme la belleza de la literatura. Sin ti no hubiera llegado hasta aquí.
Juana, thank you for creating the magnificent cover art for this thesis.