MTL FALL DAYS 2025

This time at the MPI for Polymer Research in Mainz!

Join us as we come together with the MtL community to share projects, spark new ideas, and celebrate science! Find all the details below. 

Accommodation

Accommodation at the Holiday Inn, the niu Mood is provided to all the PhD candidates. 

Address
Holiday Inn, the niu Mood
Mombacher Straße 6
55122 Mainz

Check in from 3 pm; Check out until 12 pm

Getting there: walk 10 min from main station to hotel 
 

Venue

Our friendly hosts this time will be our Fellows at the Max Planck Institute for Polymer Research! 

Address
Hermann Staudinger Lecture Hall at the MPI for Polymer Research
Ackermannweg 10
55128 Mainz

On Monday, please arrive at the venue 8:30 latest for the check-in! 

Getting there: 

• Public transport leaves from main station to the MPI; you could take one of the following connections: take the bus 630 or alternatively , take bus 153 
   
• By walking, it’ll be around 50 min from the hotel to the MPI for Polymer Reseach
   

Food

• Breakfast will be provided at the hotel on both days
• Lunch will be provided at the MPI for Polymer Research
• Dinner is self-organized
   

Lab visits

More information coming soon!

Questions? Contact us:

Email: mattertolife@maxplanckschools.de

Phone: Sarah Wypysek +49 ‭171 4170873‬
 

Program Agenda

 

Poster Session

Monday 15:00 - 18:00 and Tuesday 10:00

Poster 1: Effect of pharmacological drugs on contractility of human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CM)

Yogesh Pratap

Human-induced pluripotent stem cell–derived cardiomyocytes (hiPSC-CMs) provide an important model to study cardiac contractility and its regulation, particularly in response to mechanical and pharmacological cues. Here, we investigated how substrate stiffness can influence force generation in hiPSC-CMs using traction force microscopy on polyacrylamide gels of defined Young’s modulus (YM). We quantified the traction stress applied by hiPSC-CMs when incubated on gels of YM 1200 and 9000 Pa. Consistent with the known mechanosensitivity of cardiomyocytes, the traction force applied by hiPSC-CMs on the 9000 Pa substrate was observed to be twice as high as on the 1200 Pa substrate. We also identified that the shape of the contraction could be well described by a Gaussian function, with variance providing an estimate of the total time to complete one contraction. Further analysis of the stress fields generated by single cells at baseline and upon incubation with pharmacological drugs revealed signatures consistent with their known effects on the human heart. Epinephrine, an agonist of β-adrenergic receptors, increased contraction frequency but mildly decreased traction stress, indicating its direct effect on ion channels and action potential buildup. Mavacamten, a myosin ATPase inhibitor, suppressed stress generation by 12-fold compared to control, while keeping beating frequency and cell size unchanged. Omecamtiv mecarbil, a direct myosin activator, significantly increased contraction time while maintaining beating frequency, but traction stress decreased. In all cases, contraction shapes differed markedly from control, and the goodness of fit to the Gaussian model decreased significantly, highlighting the need for alternative models to describe contraction dynamics under drug treatment. Overall, this study highlights the importance of TFM in quantifying stress fields from displacement fields with higher precision compared to other conventional methods and provides opportunities to understand drug action and precision cardiotoxicity screening.

Poster 2: Computational design of protein binders to Evi/Wls

Samuel Novak

Computational protein design methods have experienced a renaissance in recent years, which was reflected by the last Nobel Prize in Chemistry 2024. One significant area of research in protein design is the design of protein binders that can selectively bind to protein targets, which has great implications for biotechnological and pharmaceutical industries.
Wnt-pathway is one of the major signalling cascades that, when disrupted, can lead to cancer proliferation. Understanding and controlling this mechanism is of great interest in the treatment of colorectal cancer.
Here, I present my research conducted during laboratory rotation in a group of Michael Boutros at dkfz Heidelberg, under the supervision of Filip Port, where small protein binders (50 – 80 residues) were designed using state-of-the-art computational methods: BindCraft and AlphaFold3. Binders were designed to selectively bind to a transmembrane protein Evi/Wls, which is crucial for the release of Wnt proteins into the extracellular space, which are subsequently sensed by surrounding tissue cells. Best binder candidates were selected, and in vivo assays were used to determine their binding potential.

Poster 3: Evolving Interactions in Multicomponent Liquids

Sophia Hampe

Phase separation of multicomponent liquids provides a powerful framework to study cellular self-organization, from compartmentalization to the regulation of biochemical networks. A key question is how cells could have evolved the interactions among components, such as proteins, to enable efficient self-organization. While previous work has shown that interaction matrices can be evolved to control the number of coexisting phases, it remains unclear how specific compositional targets can be robustly achieved. Here, we extend the evolutionary optimization framework to investigate the robustness of evolved interaction matrices with respect to compositional control. We assess robustness along two dimensions: (i) mutation robustness, examining how small perturbations in the interaction matrix or changes in component availability affect target attainment; (ii) initial condition sensitivity, evaluating the variability of evolutionary outcomes across independent runs.

Poster 4: Search for Optimal Intermediates for Non-Equilibrium Free Energy Calculations

Chirag Verma

Free energy (FE) differences are the driving forces behind biomolecular processes. A key application of molecular dynamics (MD) simulation is therefore to calculate FE differences, e.g. between two molecules that are chemically similar or that are the same but in different states or environments. However, the involved states must have a sufficient configurational space overlap for an accurate FE difference. To increase overlap, the two end states can be connected by a sequence of virtual (alchemical) intermediates. A linear interpolation between the two end states is a simple, but not necessarily the best, way to construct such intermediates. Recently, in the context of equilibrium simulations, the "optimal" nonlinear intermediate was derived using a variational approach.
Here, we search for the "optimal" intermediate in the context of non-equilibrium FE calculations based on the Crooks Fluctuation Theorem. To this end, we ran a grid search for the optimal intermediate using a Monte Carlo-based fast growth scheme on simple 1D model systems. The "optimal" intermediate is the one that results in the minimum mean squared deviation from the actual FE difference of the model system. We demonstrate that the recently derived optimal intermediate for equilibrium schemes can be recovered.

Poster 5: Engineering CLIP-tag2 self-labelling protein for enhanced labelling kinetics and live-cell applications

Anamarija Pišpek

Self-labelling proteins (SLPs) like SNAP-tag and HaloTag enable specific labelling of fusion proteins with synthetic fluorophores for live-cell imaging. While HaloTag7 and SNAP-tag2 achieve fast labelling kinetics (10⁷ M⁻¹ s⁻¹), CLIP-tag, an orthogonal SLP that reacts with benzylcytosine derivatives, suffers from slow kinetics (10⁴ M⁻¹ s⁻¹) and poor substrate permeability, limiting its utility for live-cell applications.Further optimization employed synthetic deep mutational scanning library (sDMSL) with yeast surface display screening, identifying additional beneficial mutations. The final CLIPtag2 contains 15 point mutations and a redesigned loop, achieving remarkable performance improvements: 1000-fold increased labelling kinetics (1.4 × 10⁷ M⁻¹ s⁻¹) comparable to HaloTag7 and SNAP-tag2, while maintaining orthogonality (1000-fold selectivity over competing substrates) and enhanced thermal stability (Tm ≈ 58°C).Live-cell validation in U2OS cells demonstrated CLIP-tag2's superior performance across multiple fluorophores (TMR, CPY, SiR) and subcellular localizations (nuclear, cytoskeletal, mitochondrial). CLIP-tag2 outperformed CLIPf-tag, matched or exceeded HaloTag7 labellingspeed, and showed comparable fluorescence brightness to HaloTag7. Efficient labellingoccurred even at low concentrations (20 nM) and short incubation times (1 hour), establishing CLIP-tag2 as a robust orthogonal system for multicolour live-cell imaging applications.

Poster 6: Simulating DNA Photodimerization Using Reactive Molecular Dynamics

Boris Schüpp

Pyrimidine bases in DNA can react under UV light to form cyclobutane pyrimidine dimers (CPDs), which play a crucial role in the development of skin cancer. In DNA nanotechnology, CPDs are also utilized to increase the chemical and physical stability of DNA origami by acting as covalent crosslinks between staples. Experimentally, the efficiency of CPD formation is quantified by the quantum yield—the ratio of successful dimerization events to the number of absorbed photons.
To investigate the reactivity and quantum yield of potential dimerization sites across various DNA motifs, we employ reactive molecular dynamics simulations using the Kinetic Monte Carlo / Molecular Dynamics (KIMMDY) approach. Our simulations reveal that the formation of different CPD diastereomers exhibits significantly different quantum yields. Surprisingly, the predicted quantum yield for motifs commonly found in DNA origami is substantially lower than that for comparable double-stranded DNA, which may inform improved protocols for DNA origami stabilization. Furthermore, we observe that consecutive dimerization reactions are unaffected by the presence of nearby CPDs (within five base pairs), suggesting that previously damaged DNA is not necessarily more susceptible to further UV-induced lesions.

Poster 7: Directional reconstitution of bacterial chemoreceptor Tar in GUVs

Chee Seng Man

In prokaryotes, chemoreceptors play an essential role in eliciting chemotaxis by binding to effectors and transducing signals to flagellar motor, in conjunction with various chemotaxis proteins. Chemotaxis has been studied extensively in Escherichia coli, and despite having only five chemoreceptors, they are capable of detecting a wide range of ligands directly or with the help of binding proteins. The chemoreceptor Tar is one of the two high-abundance receptors in E. coli, senses aspartate and maltose as attractants, and metal ions as repellents. In this project, we investigate different methods of inserting Tar into giant unilamellar vesicles (GUVs) in the absence of coupling protein CheW and histidine kinase CheA, and assess their insertion efficiencies. Another important aspect to consider during membrane protein reconstitution is the orientation. Overall, the chemoreceptors are alpha-helical coiled-coils of almost 40 nm in length, with the transmembrane sensing domain spanning about one-third of the length at one end, and bind to CheW and CheA at the other end in the cytoplasm. Such directionality should be maintained for subsequent evaluation on receptor activity and higher-order array formation.

Poster 8: Parameterizing O-glycans for the Martini 3 Coarse-Grained Force Field

Christina Goss

Mucin-like proteins play important roles in forming protective barriers for epithelial tissues. They are heavily glycosylated with O-glycans, which are important to the mucins' function. As these glycosylated proteins are very large, coarse-grained simulations are necessary to explore the influence of the O-glycans on mucin-like proteins function. To address this, we parameterize O-glycans for the Martini 3 coarse-grained force field.

Poster 9: Mechanical Characterization of Reconstituted Skeletal Muscles

Anna Mukhina

Reconstituted tissues are fundamental model systems in tissue engineering. They not only offer a promising platform for drug screening and the development of personalized medicine, but also serve as powerful tools for investigating the biophysical processes underlying physiological and pathological conditions. 
In this study, we modify the design of an established chamber model used for tissue generation and culture. The new setup enables us to apply controlled external forces to reconstituted muscle tissues and examine their mechanical properties. This approach helps us to isolate the biomechanical cues that drive tissue development and remodeling. It should also allow us to replicate physiologically relevant processes, such as isometric and eccentric contractions, as well as pathological changes like tissue stiffening.

Poster 10: Learning Diblock Copolymer Dynamics using Neural Operators

Octavian Ianc

We present a data-driven framework for learning the structure formation kinetics of diblock copolymers directly from consecutive trajectory snapshots of field-theoretic models using a neural ordinary differential equation solver.1 The dynamics areparametrized with a Fourier Neural Operator,2 enabling the efficient representation of both local and nonlocal effects. To extend the approach to systems with memory, arising from the configurational dynamics of the extended macromolecules, and toensure generalization across different physical model parameters, we develop a delay differential equation solver compatible with PyTorch and CUDA. Theapproach was validated on data generated using the Ginzburg-Landau and Ohta-Kawasaki models, with and without memory, demonstrating the accuracy and efficiency of the approach. We currently extend the strategy to particle-based molecular simulations data, obtained using the program SOMA.

Poster 11: Impact of Higher-order interactions in the synchronization of a system of self-propelled Kuramoto oscillators

Silvia Morales Manzano

Synchronization plays a key role in natural systems such as neuronal signaling, flocking behavior, and coordinated cellular dynamics. Recent work has shown that higher-order interactions can significantly impact collective synchronization in a system of Kuramoto-coupled oscillators. In this study, we simulate a reduced three-oscillator Kuramoto model with non-Hamiltonian, three-body coupling in a 2D, self-propelled, topologically interacting system. We uncover a novel nematic equilibrium state where oscillators align anti-parallel to each other. This state does not emerge under pairwise interactions alone. Our results demonstrate how three-body couplings can fundamentally reshape the stability landscape, leading to new and unexpected synchronized behaviors.
 

Poster 12: Electromechanical mapping of atrial fibrillation

Vitalii Grigorev

Atrial fibrillation is the most common heart rhythm disorder, which can develop into heart failure or facilitate the ventricular fibrillation - both severe and often lethal pathological conditions. That motivates an extensive studies of its mechanisms both in clinical practice and fundamental research.
From the biophysical prospective, atrial fibrillation is a contraction governed by a chaotic pattern of multiple spiral waves of excitation. One can image this pattern on the surface of the heart by using voltage-sensitive fluorescent dyes; as well as the "3D spiral waves" of heart contraction inside the tissue by using ultrasound. Our group successfully did it for ventricular fibrillation a few years ago. Now it is time for atria!
This master thesis gives first an outlook of how the mapping of arrhythmias is performed today, especially focusing on the ex-vivo optical mapping and ultrasound techniques. Then it introduces the adaptation of those methods (esp. ultrasound) to the atrial tissue, which in the future might become a non-invasive alternative to the current fibrillation mapping used in clinical practice.
 

Poster 13: Trimethoprim‑Induced Proximity: A Small‑Molecule Switch for CAR‑T Control

Laurin Schulze-Forster

Chimeric antigen receptor (CAR) ‑ T cell therapy has transformed the treatment of hematologic malignancies. Yet uncontrolled activation can cause severe side effects and premature T‑cell exhaustion. To address these challenges, we have developed a new synthetic biology module that implements the FDA‑approved antibiotic trimethoprim (TMP) as chemical inducer of proximity (CIP). This approach repurposes TMP, a well-characterized drug, to modulate CAR activity.Our module is based on split E. coli dihydrofolate reductase (eDHFR), compromising the N‑terminal fragment (ΔeDHFR, residues 1‑145) and a small C‑terminal peptide (eDC‑pep, residues 146‑159). In the absence of TMP, the fragments remain separate and ΔeDHFR exhibits a degron‑like activity, being degraded due to its structural instability, whereas the eDC‑pep remains stable. Addition of TMP (0.025–10 µM) drives dose‑dependent complementation of the fragments, restoring protein stability and enabling dimerization in mammalian cells. This interaction is fully reversible upon TMP washout, providing a tunable switch with a wide dynamic range.We incorporated the split eDHFR pair into a splitCAR architecture, positioning each fragment on separate signaling modules. First activation assays in Jurkat T cells demonstrated TMP‑dependent restoration of CAR‑mediated signaling, while basal activity remained minimal. These findings validate the TMP-based CIP as a promising tool for enhancing the safety of CAR-T cell therapy and facilitate future clinical applications.
 

Poster 14: Building a Minimal Pyrenoid in E. coli: A Step Toward Synthetic Carbon Concentration Mechanisms

Ava Jahad Mohammadi

Enhancing carbon fixation efficiency is a key strategy for addressing the growing demands of agriculture. Pyrenoids are organelle-like structures that improve carbon fixation by concentrating CO₂ around RubisCO through liquid–liquid phase separation, mediated by the linker protein EPYC1. Previous studies have demonstrated that directly fusing EPYC1 to RubisCO can reconstitute a simplified, functional pyrenoid in vitro. This study investigates the in vivo implementation of this minimal system in Escherichia coli.

Poster 15: RNA design for synthetic cells

Fenja Murken

RNA origami enables co-transcriptional folding from a single RNA strand, offering significant advantages for nanostructure design. As a foundational step toward synthetic life, we have developed a functional RNA nanopore. At 2.8 kb, this represents the largest RNA structure designed to date. For membrane insertion, we introduce a modular system based on short RNA sequences taking advantage of RNA’s unique interactions with lipids. These aptamers serve as membrane-anchoring sites, enabling targeted insertion. To optimize our designs, a deeper understanding of RNA folding is essential, making structural studies a key component of our approach.

Poster 16: Archaecombisomes: biomimetic hybrid vesicles constructed from ionically linked comb copolymers and archaeal lipids

Juan Figueroa Macias

The development of biomimetic hybrid vesicles that integrate synthetic polymers with natural lipids represents a promising approach to both reproduce and expand the functional complexity of biological membranes. Here, we introduce archaeacombisomes, a new class of hybrid compartments constructed from ionically-linked comb copolymers and archaeal lipids. The polymer backbone, CBAA-co-DMAPAA, was synthesized via single electron transfer living radical polymerization (SET-LRP) and characterized by 1H-NMR and GPC. Phosphate-based ligands, including a vertically crosslinked dimer, were synthesized and confirmed by 1H-, 13C-, 31P-NMR and ESI-MS analyses. Giant unilamellar vesicles (6–8 µm) were obtained by thin film rehydration using various ligand mixtures and combinations with archaeal lipids from Haloferax volcanii. Membrane structure and dynamics were assessed by LAURDAN generalized polarization and DPH fluorescence anisotropy. Incorporation of ligand 2 (with a terminal unsaturation) or archaeal lipids resulted in increased membrane disorder, while the crosslinked ligand 3 induced higher generalized polarization values and significantly elevated apparent microviscosity, consistent with a more tightly packed hydrophobic core. Vesicle assembly occurred robustly under physiological pH and in the presence of low concentrations of divalent cations, but was inhibited at high NaCl concentrations, highlighting the sensitivity of the system to hydration conditions. Taken together, these results establish archaeacombisomes as versatile biomimetic membranes with tunable physical properties, offering potential for applications in protein reconstitution, molecular encapsulation, membrane fusion, and the design of nano- and microscale reactors.

Poster 17: Hydrodynamically-active oily ocean surface as a universal cradle for the emergence of life

Johannes Hahmann

Geological environments that synthesize life’s building blocks, concentrate organics, and support replication and evolution are central to origin-of-life research. However, commonly proposed settings such as hydrothermal vents, tide pools, and closed basins often suffer from dilution or burial of organic material. We propose and experimentally support an alternative scenario in which life emerges on an oily, hydrodynamically active ocean surface. Organic carbon delivered by micrometeorites could have been buried, matured into petroleum-like hydrocarbons, and seeped upward to form oil slicks. These slicks accumulated in ocean gyres, where they avoided rapid dilution. Rainfall and wave action fragmented the slicks into droplets that formed stable compartments. These droplets grew by absorbing organic molecules, divided through hydrodynamic shear, and were eliminated by loss of buoyancy due to mineral accretion. We demonstrate droplet formation, growth, and fission in experiments, along with seawater encapsulation. This model offers a geophysically grounded and experimentally supported setting for life’s origin."

Poster 18: Engineering of a N-carbamylglutamate biosynthesis pathway

Luis Gutierrez Mondragon

N-carbamyl-L-glutamate (NCG)  is a 6-carbon molecule that closely resembles N-acetyl-glutamate (NAG), an important molecule for ammonia metabolism. Due to this structural similarity to NAG, a lot of different functions have been associated with NCG. Some of these functions are as an apoptotic inducer and growth inhibitor in different types of cancer, an antioxidant agent in liver and plasma in rats, an enhancer of mammalian reproductive efficiency and fetal development, or as an additive in swine production. Apart from this, one relevant function is as a treatment for hyperammonemia, which is a condition where there is an elevated concentration of ammonia in the blood. However, due to the high cost of its chemical precursors and in vitro being the only way to synthesize it, the cost of NCG is high, around $21/g. In prokaryotic organisms, NAG is an intermediate molecule needed for the production of L-arginine. Taking this into account, together with the advantages of in vivo metabolite production as cheaper initial materials, we propose an alternative and more cost-effective way of synthesizing this compound.

Poster 19: Cellular Uptake of DNA Condensates

Ana Valenzuela

Cells rely on intricate biochemical networks to sense and respond to their environment, yet studying these networks remains challenging due to their inherent complexity. DNA-based reaction networks provide a bottom-up framework that can recapitulate key features of natural systems and be engineered to reprogram cellular functions. Achieving such reprogramming requires efficient intracellular delivery; however, conventional nanocarriers often demand extensive optimization and are costly to produce. Self-assembled DNA condensates, formed via liquid–liquid phase separation (LLPS) of long single-stranded DNA polymers, offer an easily produced and programmable alternative that integrates delivery and information-processing capabilities into a single entity. Here, we investigate their cellular uptake to evaluate their potential as intracellular biosensors.

Poster 20: Peptide-Induced Intracellular LLPS through Complex Coacervation

Emirhan Koca

Cells employ liquid–liquid phase separation (LLPS) to organize biochemical reactions into membraneless compartments such as nucleoli and stress granules.[1] This process is typically mediated by intrinsically disordered proteins (IDPs) and RNA, where entropic and electrostatic interactions drive the formation of dynamic condensates with liquid-like properties. Minimal synthetic peptides have recently been shown to mimic such behavior,[2] yet these systems phase-separate only ex vitro, as they are not transported into cells as soluble monomers and therefore lack cell-instructed droplet formation. Here, we present a branched hexameric peptide platform in which positively charged soluble monomers can be readily conjugated for cellular uptake and undergo LLPS in the presence of negatively charged biomolecules such as nucleic acids or ATP. This design enables controlled intracellular condensate formation, directly linking peptide sequence and structure to selective supramolecular interactions. The condensates in turn modulate cellular processes, although their precise dynamics and downstream consequences remain to be fully defined. Collectively, these findings suggest our system as a programmable platform with future potential in catalytic reactions, synthetic biology, and therapeutic strategies for targeting diseased cells.