Structure and Dynamics of Simple Microclusters

A complete configurational study for the bound states of Ne trimers

The structural properties and the energetics of the ground and the excited bound states of Ne(3) for zero total angular momentum are examined using different modelings for the two-body interactions. We employ a method consisting of a variational approach with a distributed Gaussian functions (DGF) basis set expansion. We discuss at length the advantages and possible limitations of such an approach, comparing it to other methods which have been applied in the literature to the same system. The DGF method turns out to be very accurate in giving us the bound states energetics and also provides in a natural way a convincing pictorial description of all the states, including those with dominant linear configurations. Additional bound states are found for the Ne(3) system with respect to those indicated in previous works and we suggest a "stabilization" procedure that can be used to assess the truly bound nature of a state. Some considerations on the relative reliability of the examined two-body interactions are also reported.

Applicability of the Hunjan-Ramaswamy global optimization method

Int. J. Mol. Sci. 3, 30 (2002)]; Phys. Rev. E 66, 046704 (2002)]] a method for global optimization, according to which the global minimum of a potential V(f) can be found, if a potential V(i) (with a known global minimum) is transformed adiabatically in time to V(f) , with the use of a switching function of time g (t) , which interpolates between 0 and 1, and lies in the [0,1] interval. In the present work, the method is examined in detail. With the use of a very simple one-dimensional hypothetical potential, it is shown that the potential transformation may not always be followed by a global minimum transformation, which indicates that the method may not always be safely applied in determining the global minimum. An attempt to improve the method is made by allowing the switching function g (t) to take values outside the [0,1] interval. This improved method is shown to succeed in three different realistic problems, for which the original method fails.

Replacement equivalence of H- and argon in small (Ar)nH- clusters from optimized structure calculations

The structural properties of some of the smaller ionic clusters of argon atoms containing the atomic impurity H-, ArnH- with n from 2 up to 7, are examined using different modeling for the interactions within each cluster and by employing different theoretical treatments, both classical and quantum, for the energetics. The same calculations are also carried out for the corresponding neutral homogeneous clusters Ar(n+1). The results of the calculations, the physical reliability of the interactions modeling, and the similarities and the difference between the anionic and the neutral complexes are discussed in some detail. The emerging picture shows that, due to specific features of the employed atom-atom potentials, the ArnH- and Ar(n+1) clusters present very similar structures, where the H- dopant substitutes for one of the outer Ar atoms but does not undergo as yet solvation within such small clusters.

Folding of the GB1 hairpin peptide from discrete path sampling

The discrete path sampling technique is used to calculate folding pathways of the 16-amino acid beta hairpin-forming sequence from residues 41-56 of the B1 domain of protein G. The folding time is obtained using master equation dynamics and kinetic Monte Carlo simulations, and the time evolution of different order parameters and occupation probabilities of groups of minima are calculated and used to characterize intermediates on the folding pathway.

The size of neutral free clusters as manifested in the relative bulk-to-surface intensity in core level photoelectron spectroscopy

A new approach for obtaining an estimate of the effective size of the free neutral clusters is proposed. The approach relies on an experimental measure of the surface and interior or "bulk" cluster atoms provided by the x-ray photoelectron spectroscopy and on a model for the attenuation of photoelectrons ejected from the bulk of the cluster as the result of the ionizing irradiation. The experimental part gives the ratio of the electron signal from the bulk cluster atoms to that from the cluster surface atoms for a wide range of cluster sizes and electron kinetic energies. The attenuated response of the bulk atoms is modeled using an exponential law with the cluster size and kinetic-energy-dependent electron escape depth as parameters. For the experimental size range, model-based calculations for Ar, Kr, and Xe clusters are presented. The cluster size estimates obtained from comparison of the model calculations and experimental results agree well with those determined from the parameters of the cluster creation process. The combination of experiment and modeling also makes it possible to estimate the effective escape depth for electron propagation in free clusters. For Ar, Kr, and Xe clusters of varying mean size, absolute determination of the surface and bulk electron binding energies of the core levels used in the experiments has also been made.

Ionization of Clusters in Intense Laser Pulses through Collective Electron Dynamics

The motion of electrons and ions in medium-sized rare gas clusters ( approximately 1000 atoms) exposed to intense laser pulses is studied microscopically by means of classical molecular dynamics using a hierarchical tree code. Pulse parameters for optimum ionization are found to be wavelength dependent. This resonant behavior is traced back to a collective electron oscillation inside the charged cluster. It is shown that this dynamics can be well described by a driven and damped harmonic oscillator allowing for a clear discrimination against other energy absorption mechanisms.

New space warping method for the simulation of large-scale macromolecular conformational changes

A space warping method, facilitating the modeling of large-scale conformational changes in mesoscopic systems, is presented. The method uses a set of "global (or collective) coordinates" that capture overall behavior, in conjunction with the set of atomic coordinates. Application of the space warping method to energy minimization is discussed. Several simulations where the method is used to determine the energy minimizing structures of simple central force systems are analyzed. Comparing the results and behavior of the space warping method to simulations involving atomic coordinates only, it is found that the space warping method scales better with system size and also finds lower minima when the potential energy surface has multiple minima. It is shown that the transformation of [Ala16]+ in vacuo from linear to globular is captured efficiently using the space warping method.

Structural relaxation in atomic clusters: master equation dynamics

The role of the potential energy landscape in determining the relaxation dynamics of model clusters is studied using a master equation. Two types of energy landscape are examined: a single funnel, as exemplified by 13-atom Morse clusters, and the double funnel landscape of the 38-atom Lennard-Jones cluster. Interwell rate constants are calculated using Rice-Ramsperger-Kassel-Marcus theory within the harmonic approximation, but anharmonic model partition functions are also considered. Decreasing the range of the potential in the Morse clusters is shown to hinder relaxation toward the global minimum, and this effect is related to the concomitant changes in the energy landscape. The relaxation modes that emerge from the master equation are interpreted and analyzed to extract interfunnel rate constants for the Lennard-Jones cluster. Since this system is too large for a complete characterization of the energy landscape, the conditions under which the master equation can be applied to a limited database are explored. Connections are made to relaxation processes in proteins and structural glasses.