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Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Several physical systems in condensed matter have been modeled approximating their constituent particles as hard objects. The hard spheres model has been indeed one of the cornerstones of the computational and theoretical description in…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
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…
Molecular dynamics simulations are typically constrained to have a fixed number of particles, which limits our capability to simulate chemical and physical processes where the composition of the system changes during the simulation time.…
The theoretical investigation of non-adiabatic processes is hampered by the complexity of the coupled electron-nuclear dynamics beyond the Born-Oppenheimer approximation. Classically, the simulation of such reactions is limited by the…
The study of many-body quantum dynamics in strongly-correlated systems is extremely challenging. To date few numerical methods exist which are capable of simulating the non-equilibrium dynamics of two-dimensional quantum systems, in part…
With the aim of establishing a framework to efficiently perform the practical application of quantum chemistry simulation on near-term quantum devices, we envision a hybrid quantum--classical framework for leveraging problem decomposition…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. In order to understand the fundamental principles which govern material behavior…
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
Molecular Dynamics (MD) simulations are a powerful tool for studying matter at the atomic scale. However, to simulate solids, an initial atomic structure is crucial for the successful execution of MD simulations, but can be difficult to…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…