Related papers: Selecting 3D Chaotic Flow States for Accelerated D…
Recent efforts have extended the flow-matching framework to discrete generative modeling. One strand of models directly works with the continuous probabilities instead of discrete tokens, which we colloquially refer to as Continuous-State…
The Cahn-Hilliard equation with an externally-prescribed chaotic shear flow is studied in two and three dimensions. The main goal is to compare and contrast the phase separation in two and three dimensions, using high-resolution numerical…
Identifying low-energy adsorption geometries on catalytic surfaces is a practical bottleneck for computational heterogeneous catalysis: the difficulty lies not only in the cost of density functional theory (DFT) but in proposing initial…
A new three dimensional approach to the chaos game representation of protein sequences is explored in this thesis. The basics of DNA, the synthesis of proteins from DNA, protein structure and functionality and sequence alignment techniques…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
In recent years, Rectified flow (RF) has gained considerable popularity largely due to its generation efficiency and state-of-the-art performance. In this paper, we investigate the degree to which RF automatically adapts to the intrinsic…
Central to our understanding of chemical reactivity is the principle of mass conservation, which is fundamental for ensuring physical consistency, balancing equations, and guiding reaction design. However, data-driven computational models…
The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for…
Image-based computational fluid dynamics (CFD) has emerged as a powerful tool to study cardiovascular flows while 2D echocardiography (echo) is the most widely used non-invasive imaging modality for diagnosis of heart disease. Here, echo is…
3D Particle Imaging Velocimetry (3D-PIV) aim to recover the flow field in a volume of fluid, which has been seeded with tracer particles and observed from multiple camera viewpoints. The first step of 3D-PIV is to reconstruct the 3D…
Chemically reacting flows are common in engineering, such as hypersonic flow, combustion, explosions, manufacturing processes and environmental assessments. For combustion, the number of reactions can be significant (over 100) and due to…
The recent advent of advanced microfabrication capabilities of microfluidic devices has driven attention towards the behavior of particles in inertial flows within microchannels for applications related to the separation and concentration…
Most earlier 3D structure-based molecular generation approaches follow an atom-wise paradigm, incrementally adding atoms to a partially built molecular fragment within protein pockets. These methods, while effective in designing tightly…
In this work, we introduce an algorithmic approach to generate microvascular networks starting from larger vessels that can be reconstructed without noticeable segmentation errors. Contrary to larger vessels, the reconstruction of…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
We extend the Balancing Domain Decomposition by Constraints (BDDC) method to flows in porous media discretised by mixed-hybrid finite elements with combined mesh dimensions. Such discretisations appear when major geological fractures are…
Diffusion and flow matching approaches to generative modeling have shown promise in domains where the state space is continuous, such as image generation or protein folding & design, and discrete, exemplified by diffusion large language…
A generative model capable of sampling realistic molecules with desired properties could accelerate chemical discovery across a wide range of applications. Toward this goal, significant effort has focused on developing models that jointly…
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…