Related papers: Grand-canonical-like molecular-dynamics simulation…
We present a fully adaptive multiresolution scheme for spatially two-dimensional, possibly degenerate reaction-diffusion systems, focusing on combustion models and models of pattern formation and chemotaxis in mathematical biology.…
We propose Adjustable Molecular Representation (AdaMR), a new large-scale uniform pre-training strategy for small-molecule drugs, as a novel unified pre-training strategy. AdaMR utilizes a granularity-adjustable molecular encoding strategy,…
Modern observations of the interstellar medium (ISM) in galaxies detect a variety of atomic and molecular species. The goal is to connect these observations to the astrochemical properties of the ISM. 3D hydro-chemical simulations attempt…
We have implemented non-ideal Magneto-Hydrodynamics (MHD) effects in the Adaptive Mesh Refinement (AMR) code RAMSES, namely ambipolar diffusion and Ohmic dissipation, as additional source terms in the ideal MHD equations. We describe in…
In this series of papers we study the structure of the atomic to molecular transition in the giant atomic-molecular complexes that are the repositories of most molecular gas in galaxies, with the ultimate goal of attaining a better…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We present a new program implementation of the gaussian process regression adaptive density-guided approach [J. Chem. Phys. 153 (2020) 064105] in the MidasCpp program. A number of technical and methodological improvements made allowed us to…
Recent progress has been made with Adaptive Multiple Importance Sampling (AMIS) methods that show improvement in effective sample size. However, consistency for the AMIS estimator has only been established in very restricted cases.…
Coordinated multi-arm manipulation requires satisfying multiple simultaneous geometric constraints across high-dimensional configuration spaces, which poses a significant challenge for traditional planning and control methods. In this work,…
Radiative transfer plays a key role in the star formation process. Due to a high computational cost, radiation-hydrodynamics simulations performed up to now have mainly been carried out in the grey approximation. In recent years,…
Diffusion of interstitial alloying elements like H, O, C, and N in metals and their continuous relocation and interactions with their microstructures have crucial influences on metals properties. However, besides limitations in experimental…
Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The non-matching properties of…
We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct…
Computing accurate rate constants for catalytic events occurring at the surface of a given material represents a challenging task with multiple potential applications in chemistry. To address this question, we propose an approach based on a…
Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…
Radiative transfer has a strong impact on the collapse and the fragmentation of prestellar dense cores. We present the radiation-hydrodynamics solver we designed for the RAMSES code. The method is designed for astrophysical purposes, and in…
We propose an adaptive regularization scheme in a variational framework where a convex composite energy functional is optimized. We consider a number of imaging problems including denoising, segmentation and motion estimation, which are…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…