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Masked diffusion models (MDMs) have emerged as a promising alternative to autoregressive models for language modeling, yet the effective design of transformer architectures for MDMs remains underexplored. In this paper, we show that…
Normalizing Flows explicitly maximize a full-dimensional likelihood on the training data. However, real data is typically only supported on a lower-dimensional manifold leading the model to expend significant compute on modeling noise.…
Markov Chain Monte Carlo (MCMC) and Belief Propagation (BP) are the most popular algorithms for computational inference in Graphical Models (GM). In principle, MCMC is an exact probabilistic method which, however, often suffers from…
We present Monte Carlo simulations of an ultra coarse-grained lipid bilayer with different number of lipids on both leaflets. In the simulations, we employ a new method for measuring the elastic parameters of the membrane, including the…
Membrane tubulation is a ubiquitous process that occurs both at the plasma membrane and on the membranes of intracellular organelles. These tubulation events are known to be mediated by forces applied on the membrane either due to motor…
A new modular code called BOUT++ is presented, which simulates 3D fluid equations in curvilinear coordinates. Although aimed at simulating Edge Localised Modes (ELMs) in tokamak X-point geometry, the code is able to simulate a wide range of…
The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer halfway, we find that as a viscosity difference across the…
Spatially developing round jet flows are fundamental to numerous engineering applications. This letter applies the wave-particle turbulence simulation (WPTS) method, a recently developed multiscale approach, to simulate a spatially…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
Roughness predominantly alters the near-wall region of turbulent flow while the outer layer remains similar. This makes it a prime candidate for the minimal-span channel, which only captures the near-wall flow by restricting the spanwise…
We present a particle method for estimating the curvature of interfaces in volume-of-fluid simulations of multiphase flows. The method is well suited for under-resolved interfaces, and it is shown to be more accurate than the parabolic…
The mechanical properties of a thin, planar material, perfused by an embedded flow network, can be changed locally and globally by the fluid transport and storage, resulting in small or large-scale deformation, such as out-of-plane…
The Worldvolume Hybrid Monte Carlo (WV-HMC) method [arXiv:2012.08468] is an efficient and versatile algorithm that mitigates the sign problem while resolving the ergodicity issues inherent in Lefschetz-thimble approaches. We focus on cases…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
We report two novel fabrication techniques, as well as spectral transmission and propagation loss measurements of the subwavelength plastic wires with highly porous (up to 86%) and non-porous transverse geometries. The two fabrication…
Wind tunnel tests of 2D rough cylinders are presented. The goal is to simulate the alternate vortex shedding in flow regimes encountered in wind engineering applications, where the full scale Reynolds number is larger than the one that can…
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on…
This paper considers particle propagation in a cylindrical molecular communication channel, e.g. a simplified model of a blood vessel. Emitted particles are influenced by diffusion, flow, and a vertical force induced e.g. by gravity or…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
A microfluidic device is constructed from PDMS with a single channel having a short section that is a thin flexible membrane, in order to investigate the complex fluid-structure interaction that arises between a flowing fluid and a…