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The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods…
Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing…
A crucial component in the curation of KB for a scientific domain (e.g., materials science, foods & nutrition, fuels) is information extraction from tables in the domain's published research articles. To facilitate research in this…
Microchip electrokinetic methods are capable of increasing the sensitivity of molecular assays by enriching and purifying target analytes. However, their use is currently limited to assays that can be performed under a high external…
Letting free polymers diffuse from solution into a crosslinked polymer gel is often a crucial processing step in the synthesis of multiphase polymer-based gels, e.g., core-shell microgels. Here we use coarse-grained molecular dynamics…
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrating Kramers' theory with Bell's equation,…
Extensive investigations have been and are being carried out on a stiff clay from an underground research laboratory located at Mol (Belgium) called Boom clay, in the context of research into deep nuclear waste disposal. Suction effects in…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
We report on novel ferrogels derived from polysaccharides (sodium alginate and chitosan) with embedded iron oxide nanoparticles synthesized in situ and their combination with thermally responsive poly (N-isopropylacrylamide) for…
Particle methods based on evolving the spatial derivatives of the solution were originally introduced to simulate reaction-diffusion processes, inspired by vortex methods for the Navier--Stokes equations. Such methods, referred to as…
Developing a quantitative understanding of wave plasma processes in the lower ionosphere requires a reasonably accurate theoretical description of the underlying physical processes. For such highly collisional plasma environment as the…
With renewed interest in CO2 separations, carbon molecular sieving (CMS) membrane performance evaluation requires diffusion coefficients as inputs to have reliable estimate of the permeability. An optimal material is desired to have both…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…
We address a challenge of active flow control: the optimization of many actuation parameters guaranteeing fast convergence and avoiding suboptimal local minima. This challenge is addressed by a new optimizer, called explorative gradient…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Efficient exploration of the chemical space to search the candidate drugs that satisfy various constraints is a fundamental task of drug discovery. Advanced deep generative methods attempt to optimize the molecules in the compact latent…
In the present work, crystallization in melts and poor-solvent solutions of semiflexible polymers with different concentration was studied by means of dissipative particle dynamics simulation technique. We use a coarse-grained polymer model…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…