6 papers
Solubility prediction of organic molecules with molecular dynamics simulations
Zoran Bjelobrk, Dan Mendels, Tarak Karmakar +2
We present a molecular dynamics simulation method for the computation of the solubility of organic crystals in solution. The solubility is calculated based on the equilibrium free…
Blind search for complex chemical pathways using Harmonic Linear Discriminant Analysis
Valerio Rizzi, Dan Mendels, Emilia Sicilia +1
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Expe…
Finding Efficient Collective Variables: The Case of Crystallization
Yue-Yu Zhang, Haiyang Niu, GiovanniMaria Piccini +2
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…
Metadynamics with Discriminants: a Tool for Understanding Chemistry
GiovanniMaria Piccini, Dan Mendels, Michele Parrinello
We introduce an extension of a recently published method\cite{Mendels2018} to obtain low-dimensional collective variables for studying multiple states free energy processes in chem…
Folding a Small Protein Using Harmonic Linear Discriminant Analysis
Dan Mendels, Giovannimaria Piccini, Z. Faidon Brotzakis +2
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 plethor…
Path collective variables without paths
Dan Mendels, GiovanniMaria Piccini, Michele Parrinello
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…