925 citations · 3.1k across the 34 of their papers we have counts for
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Non-equilibrium generalized Langevin equation for multi-dimensional observables
Benjamin J. A. Héry, Lucas Tepper, Andrea Guljas +4
The Mori-Zwanzig formalism is a powerful theoretical framework for deriving equations of motion for coarse-grained observables in the form of generalized Langevin equations (GLEs)…
On the origin of Phase Transitions in the absence of Symmetry-Breaking
Giulio Pettini, Matteo Gori, Roberto Franzosi +2
In this paper we investigate the Hamiltonian dynamics of a lattice gauge model in three spatial dimension. Our model Hamiltonian is defined on the basis of a continuum version of a…
Supersymmetric Langevin equation to explore free energy landscapes
Alessandro Mossa, Cecilia Clementi
The recently discovered supersymmetric generalizations of Langevin dynamics and Kramers equation can be utilized for the exploration of free energy landscapes of systems whose larg…
Hamiltonian dynamics of homopolymer chain models
Alessandro Mossa, Marco Pettini, Cecilia Clementi
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to repr…
Topological and energetic factors: what determines the structural details of the transition state ensemble and "on-route" intermediates for protein folding? An investigation for small globular proteins
Cecilia Clementi, Hugh Nymeyer, Jose' Nelson Onuchic
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast f…
Hamiltonian dynamics and geometry of phase transitions in classical XY models
M. Cerruti-Sola, C. Clementi, M. Pettini
The Hamiltonian dynamics associated to classical, planar, Heisenberg XY models is investigated for two- and three-dimensional lattices. Besides the conventional signatures of phase…
Folding Lennard-Jones proteins by a contact potential
Cecilia Clementi, Michele Vendruscolo, Amos Maritan +1
We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like h…
Protein Design is a Key Factor for Subunit-subunit Association
Cecilia Clementi, Paolo Carloni, Amos Maritan
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simpl…
Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
Cecilia Clementi, Amos Maritan, Jayanth R. Banavar
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the dete…