Instantaneous normal mode analysis as a probe of cluster dynamics

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer

The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm^-1 from the PC, 13 cm^-1 from the MTP, and 47 cm^-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm^-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ₀² from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)₃. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ₀² is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including P_II, β, α_R, and α_L), whereas that covered by the MTP-based simulations is dominated by P_II with some contributions from β and α_R. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.

Ab Initio Transient Vibrational Spectral Analysis

Pump probe spectroscopy techniques have enabled the direct observation of a variety of transient molecular species in both ground and excited electronic states. Time-resolved vibrational spectroscopy is becoming an indispensable tool for investigating photoinduced nuclear dynamics of chemical systems of all kinds. On the other hand, a complete picture of the chemical dynamics encoded in these spectra cannot be achieved without a full temporal description of the structural relaxation, including the explicit time-dependence of vibrational coordinates that are substantially displaced from equilibrium by electronic excitation. Here we present a transient vibrational analysis protocol combining ab initio direct molecular dynamics and time-integrated normal modes introduced in this work, relying on the recent development of analytic time-dependent density functional theory (TDDFT) second derivatives for excited states. Prototypical molecules will be used as test cases, showing the evolution of the vibrational signatures that follow electronic excitation. This protocol provides a direct route to assigning the vibrations implicated in the (photo)dynamics of several (photoactive) systems.

A whole-path importance-sampling scheme for Feynman path integral calculations of absolute partition functions and free energies

Using Feynman path integrals, a molecular partition function can be written as a double integral with the inner integral involving all closed paths centered at a given molecular configuration, and the outer integral involving all possible molecular configurations. In previous work employing Monte Carlo methods to evaluate such partition functions, we presented schemes for importance sampling and stratification in the molecular configurations that constitute the path centroids, but we relied on free-particle paths for sampling the path integrals. At low temperatures, the path sampling is expensive because the paths can travel far from the centroid configuration. We now present a scheme for importance sampling of whole Feynman paths based on harmonic information from an instantaneous normal mode calculation at the centroid configuration, which we refer to as harmonically guided whole-path importance sampling (WPIS). We obtain paths conforming to our chosen importance function by rejection sampling from a distribution of free-particle paths. Sample calculations on CH4 demonstrate that at a temperature of 200 K, about 99.9% of the free-particle paths can be rejected without integration, and at 300 K, about 98% can be rejected. We also show that it is typically possible to reduce the overhead associated with the WPIS scheme by sampling the paths using a significantly lower-order path discretization than that which is needed to converge the partition function.

Effect of confinement on the mode dynamics of dipole clusters

Dynamical properties of colloidal clusters composed of paramagnetic beads are presented. The clusters were trapped either in a parabolic trough or in a hard-wall confinement. In order to access the dynamics of the ensembles, the instantaneous normal mode (INM) approach is utilized, which uses cluster configurations as an input. The peaks in the mode spectra weaken when the system size is increased and when the coupling strength is lowered. The short-time diffusive properties of the clusters are deduced using the INM technique. It is found that angular diffusion is always larger than radial diffusion regardless of the shape of the external trap. Further, short-time diffusion seems to be almost independent of the coupling strength in the solid regime, but decreases with increasing packing fraction and size of the ensembles. In general, it is found that diffusion is larger for parabolically confined than for hard-wall trapped clusters.

Phase space theory of evaporation in neon clusters: the role of quantum effects

Unimolecular evaporation of neon clusters containing between 14 and 148 atoms is theoretically investigated in the framework of phase space theory. Quantum effects are incorporated in the vibrational densities of states, which include both zero-point and anharmonic contributions, and in the possible tunneling through the centrifugal barrier. The evaporation rates, kinetic energy released, and product angular momentum are calculated as a function of excess energy or temperature in the parent cluster and compared to the classical results. Quantum fluctuations are found to generally increase both the kinetic energy released and the angular momentum of the product, but the effects on the rate constants depend nontrivially on the excess energy. These results are interpreted as due to the very few vibrational states available in the product cluster when described quantum mechanically. Because delocalization also leads to much narrower thermal energy distributions, the variations of evaporation observables as a function of canonical temperature appear much less marked than in the microcanonical ensemble. While quantum effects tend to smooth the caloric curve in the product cluster, the melting phase change clearly keeps a signature on these observables. The microcanonical temperature extracted from fitting the kinetic energy released distribution using an improved Arrhenius form further suggests a backbending in the quantum Ne(13) cluster that is absent in the classical system. Finally, in contrast to delocalization effects, quantum tunneling through the centrifugal barrier does not play any appreciable role on the evaporation kinetics of these rather heavy clusters.

Zwanzig-Mori projection operators and EEG dynamics: deriving a simple equation of motion

We present a macroscopic theory of electroencephalogram (EEG) dynamics based on the laws of motion that govern atomic and molecular motion. The theory is an application of Zwanzig-Mori projection operators. The result is a simple equation of motion that has the form of a generalized Langevin equation (GLE), which requires knowledge only of macroscopic properties. The macroscopic properties can be extracted from experimental data by one of two possible variational principles. These variational principles are our principal contribution to the formalism. Potential applications are discussed, including applications to the theory of critical phenomena in the brain, Granger causality and Kalman filters.

PACS code: 87.19.lj

Melting scenario in metallic clusters

The isothermal Brownian-type molecular dynamics simulation has been applied to study the melting behavior of bimetallic clusters. It was found that the specific heat and Lindermann-like parameter customarily used in bulk system to describe solid-liquid transition show incongruity in the predicted melting temperature T(melt). The underlying mechanisms that lead to the incompatibility of T(melt) separately deduced from these two quantities were analyzed further. To gain insight into the melting behavior, we calculated in addition the velocity autocorrelation function and its Fourier transform, the power spectrum, and extracted from them the T(melt). It appears that the T(melt) inferred from the latter quantities is closer to that deduced from the principal peak position of specific heat. Two bimetallic clusters, namely, Ag(1)Cu(13) and Au(1)Cu(13), were selected for a thorough investigation. In the context of cluster morphology, we scrutinized the atomic distributions of Ag(1)Cu(13), Au(1)Cu(13), and Cu(14) and effected a comparative study between a bimetallic cluster and a pure cluster so as to learn from comparison the differences in the thermal reaction of atoms, in particular, the impurity atom in the bimetallic cluster. On analyzing the dynamical data, we observed at a lower temperature (T<<T(melt)) migrational relocation of atoms whose dynamics was superimposed at an intermediate temperature (T<T(melt)) by permutations between atoms, and at a higher temperature (T approximately T(melt)), liquidlike or even gaslike behavior.

Relaxation and Short Time Dynamics of Bulk Liquids and Fluids Confined in Spherical Cavities and Slit Pores

The density of states for bulk and confined fluids have been modeled using a recently proposed gamma distribution (Krishnan, S. H.; Ayappa, K. G. J. Chem. Phys. 2004, 121, 3197). The gamma distribution results in a closed form analytical expression for the velocity autocorrelation function and the relaxation time of the fluid. The two parameters of the gamma distribution are related analytically to the second and fourth frequency moments of the fluid using short time expansions. The predictions by the proposed gamma model are compared with the velocity autocorrelation functions obtained using the theory of instantaneous normal modes (INMs) and from molecular dynamics simulations. The model is applied to a bulk soft sphere liquid and fluids confined in a spherical cavity and slit-shaped pores. The gamma model is able to capture the resulting changes in relaxation time due to changes in density and temperature extremely well for both the bulk liquid and confined inhomogeneous fluid situations. In all cases, the predictions by the gamma model are superior to those obtained from the INM theory. In the case of the fluid confined in a slit pore, the loadings were obtained from a grand canonical Monte Carlo simulation where the pore is equilibrated with a bulk fluid. This is similar to a confinement situation in a surface force apparatus. The predicted relaxation times vs pore widths from the gamma model are seen to accurately capture the oscillations due to formation and disruption of layers within the slit pore.

Structural Behavior and Self-Assembly of Lennard-Jones Clusters on Rigid Surfaces

The phase behavior and surface pattern formation for intermediate size Lennard-Jones clusters on rigid surfaces are examined. We use a parallel tempering Monte Carlo algorithm, in the canonical ensemble. Tempering is done over the temperature domain in most of the calculations. A two-dimensional temperature and Hamiltonian tempering algorithm is also implemented, to examine its usefulness in investigating this type of problem. In general, we observe gas phase systems as they undergo a condensation transition on the surface, followed by a freezing transition. The final solid state pattern formed by the cluster on the surface is the result of a number of competing effects. First, there is a competition between attraction within the cluster and that between cluster and surface atoms. Second, a monolayer of Lennard-Jones atoms tends to pack in a hexadic geometry. This geometry is frustrated on a surface with a different symmetry. The molecular organization of the substrate has a serious impact on the cluster packing. The surface morphology and the size mismatch between cluster and surface atoms, along with the relative interaction strengths, determine which of the effects prevail. When the surface atoms are small enough, the interactions within the cluster determine the symmetry of the pattern. In such a case, the substrate behaves similarly to a continuous surface, and the low-temperature pattern is a hexadic monolayer. When the sizes of the surface and cluster atoms are comparable, the low-temperature adsorbed geometry mimics the substrate symmetry. On a face-centered cubic surface, face-centered cubic monolayers or droplets are obtained.

Forces due to dynamic structure in thin liquid films

The long-range surface forces arising due to dynamic structure in thin liquid films are considered. The phonon formalism is applied to analyse the contribution of the collective motions in liquid to the excess free energy and the disjoining pressure of the film. It is shown that both the intermolecular interactions and the interactions between liquid and confining phases essentially have an influence on the sign and the magnitude of the phonon component of disjoining pressure and its temperature dependence. The methods and procedures used to assess the density of vibrational states for real and model liquids are discussed. The description of several spectroscopic experimental methodics specific for investigation of thin liquid interlayers is given concurrently with experimental data revealing the dynamic structuring in the course of film thinning.