Related papers: Collective Variables for Conformational Polymorphi…
We report here a study of reversible pressure-induced structural transformation between two amorphous forms of SO$_2$: molecular at pressures below 26 GPa and polymeric above this pressure, at temperatures of 77 - 300 K. The transformation…
We investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
We investigate the application of conformable derivatives to model critical phenomena near continuous phase transitions. By incorporating a deformation parameter into the differential structure, we derive unified expressions for…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
Crystallisation is an important phenomenon which facilitates the purification as well as structural and bulk phase material characterisation using crystallographic methods. However, different conditions can lead to a vast set of different…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Phase field crystals (PFC) are a tool for simulating materials at the atomic level. They combine the small length-scale resolution of molecular dynamics (MD) with the ability to simulate dynamics on mesoscopic time scales. We show how PFC…
There is an increasing interest in the amorphous states of metal-organic frameworks (MOFs) and porous coordination polymers, which can be produced by pressure-induced amorphization, temperature-induced amorphization, melt-quenching,…
Identifying local structural motifs and packing patterns of molecular solids is a challenging task for both simulation and experiment. We demonstrate two novel approaches to characterize local environments in different polymorphs of…
Investigations of the phase diagram of biaxial liquid crystal systems through analyses of general Hamiltonian models within the simplifications of mean-field theory (MFT), as well as by computer simulations based on microscopic models, are…
We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large datasets generated in single molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Clinical research often focuses on complex traits in which many variables play a role in mechanisms driving, or curing, diseases. Clinical prediction is hard when data is high-dimensional, but additional information, like domain knowledge…
Rare event sampling is a central problem in modern computational chemistry research. Among the existing methods, transition path sampling (TPS) can generate unbiased representations of reaction processes. However, its efficiency depends on…
Well-tempered metadynamics simulations are employed to explore the phase diagram of ZIF-4, a porous crystalline metal-organic framework of industrial relevance. Despite the vast amount of experimental efforts, the phase diagram that…