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Random sequential adsorption algorithm is a popular tool for modelling structure of monolayers built in irreversible adsorption experiments. However, this algorithm becomes very inefficient when the density of molecules in a layer rises.…
Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…
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…
Lightwave pulse shaping in the picosecond regime has remained unaddressed because it resides beyond the limits of state-of-the-art techniques, either due to its inherently narrow spectral content or fundamental speed limitations in…
Capturing intricate biological phenomena often requires multiscale modeling where coarse and inexpensive models are developed using limited components of expensive and high-fidelity models. Here, we consider such a multiscale framework in…
MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…
In programming, protocols are everywhere. Protocols describe the pattern of interaction (or communication) between software systems, for example, between a user-space program and the kernel or between a local application and an online…
Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein pockets, the protein interface binding with the ligand.…
Multilayered ceramic substrates with embedded micro patterns are becoming increasingly important, for example, in harsh environment electronics and microfluidic devices. Fabrication of these embedded micro patterns, such as micro channels,…
The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…
A variety of problems in device and materials design require the rapid forward modeling of Maxwell's equations in complex micro-structured materials. By combining high-order accurate integral equation methods with classical multiple…
The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…
The ability to rapidly manufacture building blocks with specific binding interactions is a key aspect of programmable assembly. Recent developments in DNA nanotechnology and colloidal particle synthesis have significantly advanced our…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…
Properly modeling and predicting the scattering response of a metasurface is a particularly challenging task. This has been shown to be especially difficult if the metasurface supports both local and nonlocal interactions, in the form of…
Thin films are ubiquitous in modern technology and highly useful in materials discovery and design. For achieving optimal extrinsic properties their microstructure needs to be controlled in a multi-parameter space, which usually requires a…
Many suspensions contain particles with complex shapes that are affected not only by hydrodynamics, but also by thermal fluctuations, internal kinematic constraints and other long-range non-hydrodynamic interactions. Modeling these systems…
One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven…
Soft colloids are increasingly used as model systems to address fundamental issues such as crystallisation and the glass and jamming transitions. Among the available classes of soft colloids, microgels are emerging as the gold standard.…
How morphogenesis depends on cell properties is an active direction of research. Here, we focus on mechanical models of growing plant tissues, where microscopic (sub)cellular structure is taken into account. In order to establish links…