Related papers: Using Diffusion Maps to Analyze Reaction Dynamics …
Reliable predictions of surface chemical reaction energetics require an accurate description of both chemisorption and physisorption. Here, we present an empirical approach to simultaneously optimize semi-local exchange and non-local…
In this work, we aimed to replicate and extend the results presented in the DiffFluid paper[1]. The DiffFluid model showed that diffusion models combined with Transformers are capable of predicting fluid dynamics. It uses a denoising…
The vibrational motion of molecules in dissipative environments, such as solvation and protein molecules, is composed of contributions from both intermolecular and intramolecular modes. The existence of these collective modes introduces…
Understanding and prediction of the chemical reactions are fundamental demanding in the study of many complex chemical systems. Reactive molecular dynamics (MD) simulation has been widely used for this purpose as it can offer atomic details…
Change point detection has become an important part of the analysis of the single-particle tracking data, as it allows one to identify moments, in which the motion patterns of observed particles undergo significant changes. The segmentation…
The kinetics of hydrogen diffusion in C15 cubic and C14 hexagonal TiCr$_2$H$_x$ (0 < $x$ <= 4) Laves-phase hydrogen storage alloys is investigated with density functional theory (DFT) and machine learning interatomic potentials (MLIPs).…
Diffusion involving atom transport from one location to another governs many important processes and behaviors such as precipitation and phase nucleation. Local chemical complexity in compositionally complex alloys poses challenges for…
We propose an alternative method for one-dimensional continuum diffusion models with spatially variable (heterogeneous) diffusivity. Our method, which extends recent work on stochastic diffusion, assumes the constant-coefficient homogenized…
In the real world, trajectory data is often sparse and incomplete due to low collection frequencies or limited device coverage. Trajectory recovery aims to recover these missing trajectory points, making the trajectories denser and more…
A mechanism for dispersion to automatically arise from the dispersionless Whitham Modulation equations (WMEs) is presented, relying on the use of a moving frame. The speed of this is chosen to be one of the characteristics which emerge from…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
In this work, the rate law for inhomogeneous concentration distributions has been formulated, by applying spatial integration over the products of species concentrations. Reaction rates for typical reactions have been investigated by…
This letter introduces a formalism for modeling time-variant channels for diffusive molecular communication systems. In particular, we consider a fluid environment where one transmitter nano-machine and one receiver nano-machine are…
The committor functions are central to investigating rare but important events in molecular simulations. It is known that computing the committor function suffers from the curse of dimensionality. Recently, using neural networks to estimate…
In this work, we present an extensive computational study on the Ziff-Gulari-Barshad (ZGB) model extended in order to include the spatial diffusion of oxygen atoms and carbon monoxide molecules, both adsorbed on the surface. In our…
In this paper, we propose a non-parametric method for state estimation of high-dimensional nonlinear stochastic dynamical systems, which evolve according to gradient flows with isotropic diffusion. We combine diffusion maps, a manifold…
Active transport such as fluid flow is sought in molecular communication to extend coverage, improve reliability, and mitigate interference. Flow models are often over-simplified, assuming one-dimensional diffusion with constant drift.…
Most diffusion based molecular channels suffer from low information capacity due to the structure of the diffusion environment. To address this issue, this paper studies the capacity of the diffusion based molecular communication by…
Flow and diffusion models have demonstrated strong performance and training stability across various tasks but lack two critical properties of simulation-based methods: freedom of dimensionality and adaptability to different inference…
In this work, we study the propagation of wildfires using an advection--diffusion--reaction model which also includes convective and radiative heat loss. An existing model is discussed \cite{asensio_2002} and a physically consistent…