We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measure...

The equilibrium free-energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is accomplished via two independent methods: By employing an extended version of the Jarzynski equality and the inherent structure formalism. A comparison of the free...

An algorithm for fast calculation of the Coulombic forces and energies of point particles with free boundary conditions is proposed. Its calculation time scales as N log N for N particles. This novel method has lower crossover point with the full O(N(2)) direct summation than the fast multipole method. The forces obtained by our algorithm are analytical derivatives of the energy which guarantee...

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Restricted open-shell Kohn-Sham (ROKS) theory provides a powerful computational tool for calculating singlet excited state energies and dynamics. However, the possibility of multiple solutions to the ROKS equations - with the associated difficulty of automatically selecting the physically meaningful solution - limits its usefulness for intensive applications such as long-time Born-Oppenheimer m...

Wei Zhang,1,2 Patrick Palmeri,3 Pascal Quinet,3,4 Émile Biémont,3,4,* Shan Du,1,2 and Zhenwen Dai1,2,5,† 1College of Physics, Jilin University, Changchun 130021, China 2Key Lab of Coherent Light, Atomic and Molecular Spectroscopy, Ministry of Education, Changchun 130021, China 3Astrophysique et Spectroscopie, Université de Mons, B-7000 Mons, Belgium 4IPNAS (Bât. B15), Université de Liège, Sart ...

The merging of molecular beam methods with those of accelerator physics has yielded new tools to manipulate the motion of molecules. Over the last few years, decelerators, lenses, bunchers, traps, and storage rings for neutral molecules have been demonstrated. Molecular beams with a tunable velocity and with a tunable width of the velocity distribution can now be produced, and are expected to b...

We apply the phase field crystal model to study the structure and energy of symmetric tilt grain boundaries of bcc iron in 3D. The parameters for the model are obtained by using a recently developed eight-order fitting scheme [A. Jaatinen et al., (2009)]. The grain boundary free energies we obtain from the model are in good agreement with previous results from molecular dynamics simulations and...

Proton transfer rates and mechanisms are studied in mesoscopic, liquid-state, molecular clusters. The proton transfer occurs in a protonion complex solvated by polar molecules comprising the cluster environment. The rates and mechanisms of the reaction are studied using both adiabatic and non-adiabatic molecular dynamics. For large molecular clusters, the proton-ion complex resides primarily on...