Related papers: Collective Variables for Crystallization Simulatio…
The study of star clusters plays an important role in our understanding of the Universe since these systems are natural laboratories for testing theories of stellar dynamics and evolution. Particularly, globular clusters (GCs) are one of…
Variable selection in cluster analysis is important yet challenging. It can be achieved by regularization methods, which realize a trade-off between the clustering accuracy and the number of selected variables by using a lasso-type penalty.…
Cross-validation (CV) is widely used for tuning a model with respect to user-selected parameters and for selecting a "best" model. For example, the method of $k$-nearest neighbors requires the user to choose $k$, the number of neighbors,…
The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented…
The application of immersed boundary methods in static analyses is often impeded by poorly cut elements (small cut elements problem), leading to ill-conditioned linear systems of equations and stability problems. While these concerns may…
Identifying a reduced set of collective variables is critical for understanding atomistic simulations and accelerating them through enhanced sampling techniques. Recently, several methods have been proposed to learn these variables directly…
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…
We present molecular dynamics (MD) simulations results for dense fluids of ultrasoft, fully-penetrable particles. These are a binary mixture and a polydisperse system of particles interacting via the generalized exponential model, which is…
Crucial to gaining control over crystallisation in multicomponent materials or accurately modelling rheological behaviour of magma flows is to understand the mechanisms by which crystal nuclei form. The microscopic nature of such nuclei,…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is…
The formation of crystals has proven to be one of the most challenging phase transformations to quantitatively model - let alone to actually understand - be it by means of the latest experimental technique or the full arsenal of enhanced…
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…
Crystallization of proteins, specifically proteins of medical relevance, is performed for various reasons such as to understand the protein structure and to design therapies. Obtaining kinetic constants in rate laws for nucleation and…
Many rare event transitions involve multiple collective variables (CVs) and the most appropriate combination of CVs is generally unknown a priori. We thus introduce a new method, contour forward flux sampling (cFFS), to study rare events…
In the field of psychopathology, Ecological Momentary Assessment (EMA) methodological advancements have offered new opportunities to collect time-intensive, repeated and intra-individual measurements. This way, a large amount of data has…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Cross-validation (CV) is a popular approach for assessing and selecting predictive models. However, when the number of folds is large, CV suffers from a need to repeatedly refit a learning procedure on a large number of training datasets.…
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…
A widely spread method of crystal preparation is to precipitate it from a supersaturated solution. In such a process, control of solution concentration is of paramount importance. Nucleation process, polymorph selection, and crystal habits…