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Micropatterning techniques have become an important tool for the study of cell behavior in controlled microenvironments. As a consequence, several approaches for the creation of micropatterns have been developed in recent years. However,…
In this letter, we characterize experimentally the diffusiophoretic motion of colloids and lambda- DNA toward higher concentration of solutes, using microfluidic technology to build spatially- and temporally-controlled concentration…
Recent advances in generative modeling with diffusion processes (DPs) enabled breakthroughs in image synthesis. Despite impressive image quality, these models have various prompt compliance problems, including low recall in generating…
Spatio-temporal patterns emerging from an initial quiescent, uniform state is a phenomenon observed in many dynamical systems sustained far from thermodynamic equilibrium, the practical application of which has only recently begun to be…
n this work, we propose a latent molecular diffusion model that can make the generated 3D molecules rich in diversity and maintain rich geometric features. The model captures the information of the forces and local constraints between atoms…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
Radiogenomic map linking image features and gene expression profiles is useful for noninvasively identifying molecular properties of a particular type of disease. Conventionally, such map is produced in three separate steps: 1)…
Autonomous science platforms which make decisions on the fly are fundamentally changing the outlook for materials development. AI-driven schemes can effectively reduce the total number of iterations needed to arrive at the best…
We study an intricate mechanism of pattern formation in globally coupled heterogeneous oscillatory media. In anodic electrochemical etching of silicon, the electrode surface splits into two amplitude-phase regions, while all oscillators…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
We propose a hierarchical protein backbone generative model that separates coarse and fine-grained details. Our approach called LSD consists of two stages: sampling latents which are decoded into a contact map then sampling atomic…
Diffusion models have emerged as state-of-the-art generative methods for image synthesis, yet their potential as general-purpose feature encoders remains underexplored. Trained for denoising and generation without labels, they can be…
The fundamental processes of biological development are governed by multiple signaling molecules that create non-uniform concentration profiles known as morphogen gradients. It is widely believed that the establishment of morphogen…
Anisotropic collective patterns occur frequently in the morphogenesis of 2D biofilms. These patterns are often attributed to growth regulation mechanisms and differentiation based on gradients of diffusing nutrients and signalling…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
Morphogen gradients play an essential role in the spatial regulation of cell patterning during early development. The classical mechanism of morphogen gradient formation involves the diffusion of morphogens away from a localized source…
Patterns in reaction-diffusion systems often contain two spatial scales; a long scale determined by a typical wavelength or domain size, and a short scale pertaining to front structures separating different domains. Such patterns naturally…
In recent years, AI-assisted drug design methods have been proposed to generate molecules given the pockets' structures of target proteins. Most of them are atom-level-based methods, which consider atoms as basic components and generate…
Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current…
Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…