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A general and efficient framework for atomistic machine learning

Publications associées (125)

Conformation of Circular DNA in Two Dimensions

Giovanni Dietler, Guillaume Witz, Kristian Rechendorff

The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent ν is topologically invariant and equal to the self-avoiding walk value ( ...

American Physical Society2008

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

Matteo Dal Peraro

Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have re ...

2007

Molecular dynamics simulation of radiation damage in bcc tungsten

Molecular dynamics (MD) simulations are performed to assess the primary damage due to high-energy neutron irradiation in bcc tungsten. For short-range interactions two different universal potentials are used, while for long-range interactions, two empirica ...

2007

Complex network analysis of free-energy landscapes

Paolo De Los Rios, David Gfeller

The kinetics of biomolecular isomerization processes, such as protein folding, is governed by a free-energy surface of high dimensionality and complexity. As an alternative to projections into one or two dimensions, the free-energy surface can be mapped in ...

National Academy of Sciences2007

Polyelectrolyte complex formation at defined interfaces and structure formation in solution studied by analytical ultracentrifugation

Laurent Bourdillon

The interactions and structural formation of polyelectrolytes in solution and environmental stimuli-responsive water-soluble polymers are subjects of intense academic research, development, and application. An increasing number of novel materials are being ...

EPFL2006

Dynamical monopoles and dipoles in a condensed molecular system: The case of liquid water

Alfredo Pasquarello

We propose a definition for the dipole of an individual molecule in a molecular solid or fluid. This problem is currently dealt with by partitioning-according to some prescription-the continuous electron density of the condensed phase. Instead, here we foc ...

2003

Transition structure at the Si(100)-SiO2 interface

Alfredo Pasquarello, Angelo Bongiorno

We characterize the transition structure at the Si(100)-SiO2 interface by addressing the inverse ion-scattering problem. We achieve sensitivity to Si displacements at the interface by carrying out ion-scattering measurements in the channeling geometry for ...

2003

Molecular-dynamics force models for better control of energy dissipation in numerical simulations of dense granular media

Thomas Liebling, Lionel Pournin

We first describe the three-dimensional extension of the molecular-dynamics models for granular media simulations. We then discuss the known energy dissipation problem occurring when simulating dense granular media with the usual molecular-dynamics forces ...

2002

Confirmation of anomalous dynamical arrest in attractive colloids: A molecular dynamics study

Giuseppe Foffi, Francesco Sciortino

Previous theoretical simulation and experimental studies have indicated that particles with a short-ranged attraction exhibit a range of dynamical arrest phenomena. These include very pronounced reentrance in the dynamical arrest curve, a logarithmic singu ...

2002

The Role and Perspective of Ab Initio Molecular Dynamics in the Study of Biological Systems

Ursula Röthlisberger, Michele Parrinello, Paolo Carloni

A review. Ab initio mol. dynamics (MD) allows realistic simulations to be performed without adjustable parameters. In recent years, the technique has been used on an increasing no. of applications to biochem. systems. Here we describe the principles on whi ...

2002

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