Related papers: Adaptive resolution molecular dynamics simulation …
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…
The main objective of this dissertation is to present an adaptation of some finite volume methods used in the resolution of problems arising in sedimentation processes of flocculated suspensions (or sedimentation with compression). This…
This work prioritizes building a modular pipeline that utilizes existing models to systematically restore images, rather than creating new restoration models from scratch. Restoration is carried out at an object-specific level, with each…
Gravitational instabilities naturally give rise to multi-scale structure, which is difficult for traditional Eulerian hydrodynamic methods to accurately evolve. This can be circumvented by adaptively adding resolution (in the form of…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
A numerical method is presented to obtain approximate solutions to problems arising from sedimentation models. These processes are widely utilized in minery for recovering water from suspensions coming out of flotation processes. The main…
Adaptive optical correction is an efficient technique to obtain high-resolution images of the retinal surface. A main limitation of adaptive optical correction, however, is the small size of the corrected image. For medical purposes it is…
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…
This paper presents a new resolution strategy for multi-scale streamer discharge simulations based on a second order time adaptive integration and space adaptive multiresolution. A classical fluid model is used to describe plasma…
High-fidelity, high-resolution numerical simulations are crucial for studying complex multiscale phenomena in fluid dynamics, such as turbulent flows and ocean waves. However, direct numerical simulations with high-resolution solvers are…
Building on the successes of local kernel methods for approximating the solutions to partial differential equations (PDE) and the evaluation of definite integrals (quadrature/cubature), a local estimate of the error in such approximations…
Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in…
Solvation is a notoriously difficult and nagging problem for the rigorous theoretical description of chemistry in the liquid phase. Successes and failures of various approaches ranging from implicit solvation modeling through dielectric…
Chemistry occurring at or near the surfaces of aqueous droplets and thin films in the atmosphere influences air quality and climate. Molecular dynamics simulations are becoming increasingly useful for gaining atomic-scale insight into the…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Shallow free surface flows are often characterized by both subdomains that require high modeling complexity and subdomains that can be sufficiently accurately modeled with low modeling complexity. Moreover, these subdomains may change in…
Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex aqueous systems such as solid-liquid interfaces. Here, we present a machine learning…
Numerical simulation of fluids plays an essential role in modeling many physical phenomena, such as weather, climate, aerodynamics and plasma physics. Fluids are well described by the Navier-Stokes equations, but solving these equations at…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
We perform molecular dynamics simulations in order to examine the rheological transition of fluids confined in a small space. By performing finite-size scaling analysis, we demonstrate that this rheological transition results from the…