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Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Complex colloidal fluids, such as emulsions stabilized by complex shaped particles, play an important role in many industrial applications. However, understanding their physics requires a study at sufficiently large length scales while…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…