45 citations · 58 across the 7 of their papers we have counts for
7 papers
Bottom-up transient time models in coarse-graining molecular systems
G. Baxevani, V. Harmandaris, E. Kalligiannaki +1
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-typ…
Data-driven Uncertainty Quantification for Systematic Coarse-grained Models
Tangxin Jin, Anthony Chazirakis, Evangelia Kalligiannaki +2
In this work, we present methodologies for the quantification of confidence in bottom-up coarse-grained models for molecular and macromolecular systems. Coarse-graining methods hav…
Path-space variational inference for non-equilibrium coarse-grained systems
Vagelis Harmandaris, Evangelia Kalligiannaki, Markos A. Katsoulakis +1
In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latte…
The geometry of generalized force matching in coarse-graining and related information metrics
Evangelia Kalligiannaki, Vagelis Harmandaris, Markos A. Katsoulakis +1
Using the probabilistic language of conditional expectations we reformulate the force matching method for coarse-graining of molecular systems as a projection on spaces of coarse o…
Spatial multi-level interacting particle simulations and information theory-based error quantification
Evangelia Kalligiannaki, Markos A. Katsoulakis, Petr Plechac
We propose a hierarchy of multi-level kinetic Monte Carlo methods for sampling high-dimensional, stochastic lattice particle dynamics with complex interactions. The method is based…
Multilevel coarse graining and nano--pattern discovery in many particle stochastic systems
Evangelia Kalligiannaki, Markos A. Katsoulakis, Petr Plechac +1
In this work we propose a hierarchy of Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each…
Coupled coarse graining and Markov Chain Monte Carlo for lattice systems
Evangelia Kalligiannaki, Markos A. Katsoulakis, Petr Plechac
We propose an efficient Markov Chain Monte Carlo method for sampling equilibrium distributions for stochastic lattice models, capable of handling correctly long and short-range par…