Related papers: Collective Variables for Conformational Polymorphi…
The phenomenon of solidification of a substance from its liquid phase is of the greatest practical and theoretical importance, and atomistic simulations can provide precious information towards its understanding and control. Unfortunately,…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…
Crystallization is one of the most important physicochemical processes which has relevance in material science, biology, and the environment. Decades of experimental and theoretical efforts have been made to understand this fundamental…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
Crystallization, a fundamental phase transition process governing material formation in natural and industrial contexts, involves the spontaneous emergence of long-range structural order from disordered phases. This long-range periodicity…
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…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
The ability to reliably predict the structures and stabilities of a molecular crystal and its polymorphs without any prior experimental information would be an invaluable tool for a number of fields, with specific and immediate applications…
Several enhanced sampling methods such as umbrella sampling or metadynamics rely on the identification of an appropriate set of collective variables. Recently two methods have been proposed to alleviate the task of determining efficient…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
Polymorphism, the ability of a compound to crystallize in multiple distinct structures, plays a vital role in determining the physical, chemical, and functional properties of materials. Accurate identification and prediction of polymorphic…
Crystalline materials can form different structural arrangements (i.e. polymorphs) with the same chemical composition, exhibiting distinct physical properties depending on how they were synthesized or the conditions under which they…
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One…
Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. Like in all first order first transitions there is an interplay between…
We introduce a method for elucidating and modifying the functionality of systems dominated by rare events that relies on the automated tuning of their underlying free energy surface. The proposed approach seeks to construct collective…
The dynamics in a confined turbulent convection flow is dominated by multiple long-lived macroscopic circulation states, which are visited subsequently by the system in a Markov-type hopping process. In the present work, we analyze the…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…