Related papers: Intracellular Measurement-Informed Multiscale Mode…
One strategy to scale up ML-driven science is to increase wet lab experiments' information density. We present a method based on a neural extension of compressed sensing to function space. We measure the activity of multiple different…
Physics-based simulation is essential for developing and evaluating robot manipulation policies, particularly in scenarios involving deformable objects and complex contact interactions. However, existing simulators often struggle to balance…
Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Multi-modal medical imaging enables comprehensive diagnostics, yet current foundation models process 2D (e.g. X-ray) and 3D (e.g. CT) data with separate, dimensionality-specific architectures. We present MultiMedVision, a unified framework…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
Kinetic modeling of microbial growth is essential for the design, optimization, and scale-up of industrial bioprocesses. Classical empirical models often lack biologically interpretable parameters or fail to capture complex multiphasic…
We formulate a cell-scale model for the degradation of the extra-cellular matrix by membrane-bound and soluble matrix degrading enzymes produced by cancer cells. Based on the microscopic model and using tools from the theory of…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
Integrated Sensing And Communication (ISAC) has been recognized as a promising technology in the 6G communication. A realistic channel model is a prerequisite for designing ISAC systems. Most existing channel models independently generate…
Organic reaction, the foundation of modern chemical industry, is crucial for new material development and drug discovery. However, deciphering reaction mechanisms and modeling multi-molecular relationships remain formidable challenges due…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
In vitro transcription (IVT) plays a critical role in the manufacture of mRNA vaccines and therapeutics. Optimizing mRNA yield and ensuring product quality, such as capping efficiency and integrity, are essential but mechanistically…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…
The project aims to explore a novel way to design and produce cellular materials with good energy absorption and recoverability properties. Spinodoid structures offer an alternative to engineering structures such as honeycombs and foam with…
Functional aspects as well as the influence of integration technology on the system behavior have to be considered in the 3D integration design process of micro systems. Therefore, information from different physical domains has to be…
Computational multiscale methods for analyzing and deriving constitutive responses have been used as a tool in engineering problems because of their ability to combine information at different length scales. However, their application in a…
A three dimensional parallel implementation of Multiscale Mixed Methods based on non-overlapping domain decomposition techniques is proposed for multi-core computers and its computational performance is assessed by means of numerical…