Related papers: Using reweighting and free energy surface interpol…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
We develop a mathematical and numerical framework to solve state estimation problems for applications that present variations in the shape of the spatial domain. This situation arises typically in a biomedical context where inverse problems…
In this study, we incorporate configuration mapping between simulation ensembles into the successive interpolation of multistate reweighting (SIMR) method in order to increase phase space overlap between neighboring simulation ensembles.…
Solubility and interfacial energy are two fundamental parameters underlying the competitive nucleation of polymorphs. However, solubility measurement of metastable phases comes with a risk of solventmediated transformations which can render…
This paper proposes a phase space to compare the static packings of a granular system compatible to a macrostate that is set by the external stress. The nature of this phase space is analyzed, showing that the consideration of the allowed…
The histogram reweighting technique, widely used to analyze Monte Carlo data, is shown to be applicable to dynamic properties obtained from Molecular Dynamics simulations. The theory presented here is based on the fact that the correlation…
The free energy landscape responsible for crystallization can be complex even for relatively simple systems like hard sphere and charged stabilized colloids. In this work, using hard-core repulsive Yukawa model, which is known to show…
We calculate the phase behavior of hard spheres with size polydispersity, using accurate free energy expressions for the fluid and solid phases. Cloud and shadow curves, which determine the onset of phase coexistence, are found exactly by…
The presence of a phase transition in a finite system can be deduced, together with its order, from the shape of the distribution of the order parameter. This issue has been extensively studied in multifragmentation experiments, with…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
The observation of stacks of distinct layers in a colloidal or liquid mixture in sedimentation-diffusion equilibrium is a striking consequence of bulk phase separation. Drawing quantitative conclusions about the phase diagram is, however,…
Under many circumstances many soft and hard materials are present in a puzzling wealth of non-equilibrium amorphous states, whose properties are not stationary and depend on preparation. They are often summarized in unconventional "phase…
We present a new multiphase-field theory for describing pattern formation in multi-domain and/or multi-component systems. The construction of the free energy functional and the dynamic equations is based on criteria that ensure mathematical…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
Much work has been devoted to analysing thermodynamic models for solid dispersions with a view to identifying regions in the phase diagram where amorphous phase separation or drug recrystallization can occur. However, detailed partial…
Elastic MicroPhase Separation (EMPS) provides a simple route to create soft materials with homogeneous microstructures by leveraging the supersaturation of crosslinked polymer networks with liquids. At low supersaturation, network…