Statistical mechanics of crystal nuclei of hard spheres.

In the study of crystal nucleation via computer simulations, hard spheres are arguably the most extensively explored model system. Nonetheless, even in this simple model system, the complex thermodynamics of crystal nuclei can sometimes give rise to counterintuitive results, such as the recent observation that the pressure inside a critical nucleus is lower than that of the surrounding fluid, seemingly clashing with the strictly positive Young-Laplace pressure we would expect in liquid droplets. Here, we re-derive many of the founding equations associated with crystal nucleation and use the hard-sphere model to demonstrate how they give rise to this negative pressure difference.

Accurate drift-invariant single-molecule force calibration using the Hadamard variance.

Single-molecule force spectroscopy (SMFS) techniques play a pivotal role in unraveling the mechanics and conformational transitions of biological macromolecules under external forces. Among these techniques, multiplexed magnetic tweezers (MT) are particularly well suited to probe very small forces, ≤1 pN, critical for studying noncovalent interactions and regulatory conformational changes at the single-molecule level. However, to apply and measure such small forces, a reliable and accurate force-calibration procedure is crucial.

Phase behavior and crystal nucleation of hard triangular prisms.

The interplay between densification and positional ordering during the process of crystal nucleation is a greatly investigated topic. Even for the simplest colloidal model-hard spheres-there has been much debate regarding the potential foreshadowing of nucleation by significant fluctuations in either local density or local structure. Considering anisotropic particles instead of spheres adds a third degree of freedom to the self-organization process of crystal nucleation: orientational ordering.

Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.

Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here, we present a simple and generic coarse-grained model for DNA-protein and protein-protein interactions and investigate the role of the latter in the protein-induced compaction of DNA.

Fast event-driven simulations for soft spheres: from dynamics to Laves phase nucleation.

Conventional molecular dynamics (MD) simulations struggle when simulating particles with steeply varying interaction potentials due to the need to use a very short time step. Here, we demonstrate that an event-driven Monte Carlo (EDMC) approach was first introduced by Peters and de With [Phys. Rev.