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Bridging the gap between atomistic detail and continuum mechanics is a central challenge in modeling biological membranes, particularly for mesoscopic phenomena spanning large length and time scales. In this work, we introduce a new,…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
Merger trees track the hierarchical assembly of dark matter halos across cosmic time and serve as essential inputs for semi-analytic models of galaxy formation. However, conventional methods for constructing merger trees rely on ad-hoc…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
In Schiebinger et al. (2017), the authors use optimal transport of measures on empirical distributions arising from biological experiments to relate the single cell RNA sequencing profiles for induced pluripotent stem cells differentiating.…
Adaptive response to a varying environment is a common feature of biological organisms. Reproducing such features in electronic systems and circuits is of great importance for a variety of applications. Here, we consider memory models…
Results from molecular dynamics simulations of simple, structured particles capable of self-assembling into polyhedral shells are described. The analysis focuses on the growth histories of individual shells in the presence of an explicit…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
The phloem vascular system facilitates transport of energy-rich sugar and signaling molecules in plants, thus permitting long range communication within the organism and growth of non-photosynthesizing organs such as roots and fruits. The…
Nonlinear coupling between inter- and intra-element dynamics appears as a collective behaviour of elements. The elements in this paper denote symptoms such as a bacterium having an internal network of genes and proteins, a reactive droplet,…
A remarkable property of nastic, shape changing plants is their complete fusion between actuators and structure. This is achieved by combining a large number of cells whose geometry, internal pressures and material properties are optimized…
Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
Xenium, a new spatial transcriptomics platform, enables subcellular-resolution profiling of complex tumor tissues. Despite the rich morphological information in histology images, extracting robust cell-level features and integrating them…
The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and…
We investigate multicellular sender receiver systems embedded in hydrogel beads, where diffusible signals mediate interactions among heterogeneous cells. Such systems are modeled by PDE ODE couplings that combine three dimensional diffusion…
Myxococcus xanthus is a unicellular organism whose cells possess the ability to move and communicate, leading to the emergence of complex collective properties and behaviours. This has made it an ideal model system to study the emergence of…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Interactions between crawling cells, which are essential for many biological processes, can be quantified by measuring cell-cell collisions. Conventionally, experiments of cell-cell collisions are conducted on two-dimensional flat…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…