Research direction 1. Metabolic compartmentalization: harnessing biomolecular condensates. Dry lab
Membraneless intracellular assemblies, commonly referred to as biomolecular condensates, play key biological roles by compartmentalizing materials inside cells, providing (i) a unique chemical environment for biological reactions, which enables (ii) protection from unwanted and toxic compounds, and (iii) spatiotemporal control of such reactions. In the context of metabolism, these three functions are known as the pillars of metabolic compartmentalization (Fig. 1a). For example, colocalization of multiple enzymes in a pathway can enhance the rate of processing of intermediates, thereby improving the efficiency of cellular metabolism. This phenomenon is observed in purinosomes or in the pyrenoid in algae, where enzyme clustering enhances photosynthetic carbon assimilation. Thus, understanding and controlling the dynamics of biomolecular condensates has critical implications for metabolic engineering, health, agriculture, and the food industry.
This research direction extends beyond metabolism. We will investigate the efficiency and emergent behaviors of intracellular aggregates in the contexts of DNA repair and transcription—both fundamental cellular processes with critical implications for genetic engineering and health. Moreover, these condensates arise in complex, crowded environments, yet the interplay between a chemomechanically complex environment and the emergence and self-organization of condensates remains largely unexplored. Thus, we also aim to understand how these fundamental biological processes are influenced by equilibrium and out-of-equilibrium reactions, cytoplasmic flows, multicomponent interactions, and crowded, heterogeneous 3D environments.
Research direction 2. Trophic interactions in multispecies microbial communities: Shape, organization, and complex metabolic networks. Wet and dry lab.
Microorganisms typically do not live in isolation but form spatially structured multicellular communities composed of multiple species and heritable phenotypes. This spatial arrangement plays a pivotal role in influencing various biological functions, including community growth, stability, metabolite cross-feeding, and diversity. Examples include microbial colonies in soils, hosts, and large bodies of water, where trophic interactions between different bacterial species, as well as interactions with plants and phytoplankton, strongly influence carbon and nutrient cycling and food webs. Laboratory studies often focus on these microbial systems in well-mixed cultures or single-species surface-attached colonies, providing valuable insights into cellular processes but failing to capture the spatial arrangement of different cell types found in nature. To address this gap in knowledge, our lab will study the interplay between different microbial metabolic interactions, colony shape, collective behavior, and spatiotemporal organization of 2D and 3D multispecies communities in complex settings that mimic their natural environments (Fig. 2b).
To achieve this goal, we will conduct experiments to visualize real-time trophic and metabolic interactions among microbes in multispecies communities in complex environments. These interactions will include mutualistic relationships (e.g., bacteria-cyanobacteria/phytoplankton), resource competition (different bacterial species competing for the same resource), and predator-prey dynamics (e.g., myxobacteria/bdellovibrio-bacteria). To understand how these interactions influence spatiotemporal organization, collective behaviors, and colony shape, we will employ crowded environments, live imaging, metabolomics, and biophysical modeling. I anticipate that the outcomes of this new direction will extend beyond prior research and shed light on the spatial diversity and organization of multicellular and multispecies structures in real-life environments, thus bridging the gap between nature and lab experiments.
Research direction 3. Microbes in complex environments: Community response to stressors. Wet and dry lab.
In nature, bacteria face multiple challenges, from fluctuating environments, mechanical stresses, tortuous environments, and nutrient deprivation to chemical and biological stressors like antibiotics, reactive oxygen species, or bacteriophages (viruses that infect bacteria). The impact of such stressors on bacteria has been often explored using continuously mixed liquid cultures. However, bacteria face these situations in structured and extended environments, such as hosts, soils, and aquatic settings, where the cells can collectively self-organize into spatially structured communities. Despite the pivotal influence of bacterial spatial organization on diverse biological functions, how such organization is influenced by, and in turn influences, interactions with stressors remains poorly understood. These interactions are of fundamental interest in biology, ecology, and physics, and have critical implications for biogeochemistry, the environment, food, health, and industry.
To address this gap in knowledge, our aim is to unravel how microbes collectively respond to biochemical and mechanical stressors, and how this response interacts with colony shape, spatial organization, and function. To this end, we will conduct experiments exposing bacteria and cyanobacteria to various stressors in complex, crowded environments, combined with biophysical modeling. I anticipate that exploring these questions will illuminate how microbial communities adapt to fluctuating environments and stressors, thereby bridging the gap between laboratory studies and natural microbial habitats (Fig. 2c). This research direction combined with 2 will also establish a framework for controlling and engineering microbial communities according to specific needs.
Summary: My research program seeks to advance our understanding of how living matter self-organizes and functions in complex settings that mimic real-life environments. To address this overarching research direction, my lab will combine experiments and theoretical modeling. The main goal of this fully integrated approach is to understand the fundamental biophysical principles underlying self-organization and function of living systems in real-life environments, and elucidate the coupling and feedback loops between morphology, function, physiology, and stressors.
The overall development and outcome of this research plan will be greater than the sum of its parts. For instance, research directions 2 and 3 will feed each other naturally. In addition, the theoretical approaches that we will develop to tackle the questions proposed in research direction 1 will certainly inform and help to develop theoretical approaches in research directions 2 and 3. Finally, this research plan will provide opportunities to establish fruitful collaborations with multiple groups in Chemical and Biological Engineering departments, as well as in Physics, Microbiology, Applied Mathematics, Materials, and Chemistry departments.
During my PhD and postdoctoral training, I gained substantial experience in university teaching. In my independent career, I am excited to teach a range of courses central to Chemical and Biological Engineering, including Fluid Mechanics, Thermodynamics, Heat and Mass Transfer, Differential Equations, and Numerical Methods. I am enthusiastic about integrating my teaching with past and current scientific research to introduce students to cutting-edge advancements at the forefront of scientific knowledge. Additionally, I am interested in developing new courses that explore fundamental aspects at the intersection of soft and active matter, biophysics, and quantitative biology. I also aim to organize seminar series that facilitate collaboration among these communities across departments and schools, providing undergraduate and graduate students opportunities to build networks, maintain connections, and foster interdisciplinary collaborations.
Teaching has always been a central aspect of my academic journey. During my graduate studies at Universidad Carlos III in Madrid, I was fortunate to teach several problems sets in various fluid mechanics courses and conducted multiple laboratory sessions each year. This early experience was invaluable for learning how to structure classes, communicate complex ideas clearly, and engage with students. During this period, I supervised several undergraduate students on their senior theses, which greatly enhanced my mentorship skills. I learned to guide and motivate students, foster critical thinking, and design successful research projects.
After completing my PhD, I had the opportunity to teach two full courses—fluid mechanics and numerical methods—before joining Princeton University. During this time, I developed skills in course organization, exam and problem set preparation, interactive teaching methods to encourage participation and active learning, and guiding students to maximize their learning outcomes. At Princeton, I continue to mentor both undergraduate and graduate students, emphasizing scientific integrity and striving to cultivate a diverse and inclusive academic community. Over these years, teaching has been a privilege, allowing me to mentor numerous students and receive excellent teaching evaluations and awards, which has been incredibly rewarding.