Related papers: Collective Variables for Conformational Polymorphi…
Compared to pure fluids, binary mixtures display a very diverse phase behavior, which depends sensitively on the parameters of the microscopic potential. Here we investigate the phase diagrams of simple model mixtures by use of a…
In simulations, particles are traditionally treated as rigid platforms with variable sizes, shapes and interaction parameters. While this representation is applicable for rigid core platforms, particles consisting of soft platforms (e.g.…
In this article, we demonstrate a method for inducing reversible crystal-to-crystal transitions in binary mixtures of soft colloidal particles. Through a controlled decrease of salinity and increasingly dominating electrostatic…
Finding proper collective variables for complex systems and processes is one of the most challenging tasks in simulations, which limits the interpretation of experimental and simulated data and the application of enhanced sampling…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
We use computer simulations to study the microscopic dynamics of an athermal assembly of soft particles near the fluid-to-solid, jamming transition. Borrowing tools developed to study dynamic heterogeneity near glass transitions, we…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in…
We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting…
In molecular dynamics (MD) simulations, transitions between states are often rare events due to energy barriers that exceed the thermal temperature. Because of their infrequent occurrence and the huge number of degrees of freedom in…
Here we propose an NPT metadynamics simulation scheme for pressure-induced structural phase transitions, using coordination number and volume as collective variables, and apply it to the reconstructive structural transformation $B1$-$B2$ in…
We present a coarse molecular-dynamics (CMD) approach for the study of stress-induced structural transformations in crystals at finite temperatures. The method relies on proper choice of a coarse variable (order parameter, observable),…
Molecular crystals often exist in multiple competing polymorphs, showing significantly different physico-chemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
We introduce a method to obtain one-dimensional collective variables for studying rarely occurring transitions between two metastable states separated by a high free energy barrier. No previous information, not even approximated, on the…
The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e normal mode analysis, principal component and spectral analysis of…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…
Molecule- and particle-based simulations provide the tools to test, in microscopic detail, the validity of classical nucleation theory. In this endeavour, determining nucleation mechanisms and rates for phase separation requires an…
We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics of crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away…