Related papers: Collective Variables for Conformational Polymorphi…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
The glass transition is a long-standing unsolved problem in materials science. For polymers, our understanding of glass-formation is particularly poor due to the added complexity of chain connectivity and flexibility; structural relaxation…
Theoretical approaches are formulated to investigate the molecular mobility under various cooling rates of amorphous drugs. We describe the structural relaxation of a tagged molecule as a coupled process of cage-scale dynamics and…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Unsupervised machine learning methods are used to identify structural changes using the melting point transition in classical molecular dynamics simulations as an example application of the approach. Dimensionality reduction and clustering…
We develop a theory based on the method of collective variables to study the vapor-liquid equilibrium of asymmetric ionic fluids confined in a disordered porous matrix. The approach allows us to formulate the perturbation theory using an…
We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the…
Molecules can form myriad crystalline polymorphs, each with distinct properties affecting their performance across diverse applications, from pharmaceuticals to functional materials and more. Predicting the thermodynamically most stable…
Micrometre sized colloidal particles can be viewed as large atoms with tailorable size, shape and interactions. These building blocks can assemble into extremely rich structures and phases, in which the thermal motions of particles can be…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
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…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Isomerization, i.e. the rearrangement between distinct molecular configurations, is a fundamental process in chemistry. Here we demonstrate that two-dimensional Coulomb crystals can emulate molecular isomerization and be used to…
Many biological processes occur on time scales longer than those accessible to molecular dynamics simulations. Identifying collective variables (CVs) and introducing an external potential to accelerate them is a popular approach to address…
Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one…
Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here, we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of…