Identification of metastable states in peptide's dynamics

A recently developed spectral method for identifying metastable states in Markov chains is used to analyse the conformational dynamics of a four residue peptide Valine-Proline-Alanine-Leucine. We compare our results to empirically defined conformational states and show that the found metastable states correctly reproduce the conformational dynamics of the system.

Statistical mechanics of distribution networks

This thesis presents an analysis of the stability of complex distribution networks. We present a stability analysis against cascading failures. We propose a spin [binary] model, based on concepts of statistical mechanics. We test macroscopic properties of distribution networks with respect to various topological structures and distributions of microparameters. The equilibrium properties of the systems are obtained in a statistical mechanics framework by application of the replica method. We demonstrate the validity of our approach by comparing it with Monte Carlo simulations. We analyse the network properties in terms of phase diagrams and found both qualitative and quantitative dependence of the network properties on the network structure and macroparameters. The structure of the phase diagrams points at the existence of phase transition and the presence of stable and metastable states in the system. We also present an analysis of robustness against overloading in the distribution networks. We propose a model that describes a distribution process in a network. The model incorporates the currents between any connected hubs in the network, local constraints in the form of Kirchoff's law and a global optimizational criterion. The flow of currents in the system is driven by the consumption. We study two principal types of model: infinite and finite link capacity. The key properties are the distributions of currents in the system. We again use a statistical mechanics framework to describe the currents in the system in terms of macroscopic parameters. In order to obtain observable properties we apply the replica method. We are able to assess the criticality of the level of demand with respect to the available resources and the architecture of the network. Furthermore, the parts of the system, where critical currents may emerge, can be identified. This, in turn, provides us with the characteristic description of the spread of the overloading in the systems.

Quantifying the complexity of chaos in multibasin multidimensional dynamics of molecular systems

The simulated classical dynamics of a small molecule exhibiting self-organizing behavior via a fast transition between two states is analyzed by calculation of the statistical complexity of the system. It is shown that the complexity of molecular descriptors such as atom coordinates and dihedral angles have different values before and after the transition. This provides a new tool to identify metastable states during molecular self-organization. The highly concerted collective motion of the molecule is revealed. Low-dimensional subspaces dynamics is found sensitive to the processes in the whole, high-dimensional phase space of the system. © 2004 Wiley Periodicals, Inc.

Metastable de-excitation spectroscopy and density functional theory study of the selective oxidation of crotyl alcohol over Pd(111)

The extremely surface sensitive technique of metastable de-excitation spectroscopy (MDS) has been utilized to probe the bonding and reactivity of crotyl alcohol over Pd(111) and provide insight into the selective oxidation pathway to crotonaldehyde. Auger de-excitation (AD) of metastable He (23S) atoms reveals distinct features associated with the molecular orbitals of the adsorbed alcohol, corresponding to emission from the hydrocarbon skeleton, the O n nonbonding, and C═C π states. The O n and C═C π states of the alcohol are reversed when compared to those of the aldehyde. Density functional theory (DFT) calculations of the alcohol show that an adsorption mode with both C═C and O bonds aligned somewhat parallel to the surface is energetically favored at a substrate temperature below 200 K. Density of states calculations for such configurations are in excellent agreement with experimental MDS measurements. MDS revealed oxidative dehydrogenation of crotyl alcohol to crotonaldehyde between 200 and 250 K, resulting in small peak shifts to higher binding energy. Intramolecular changes lead to the opposite assignment of the first two MOs in the alcohol versus the aldehyde, in accordance with DFT and UPS studies of the free molecules. Subsequent crotonaldehyde decarbonylation and associated propylidyne formation above 260 K could also be identified by MDS and complementary theoretical calculations as the origin of deactivation and selectivity loss. Combining MDS and DFT in this way represents a novel approach to elucidating surface catalyzed reaction pathways associated with a “real-world” practical chemical transformation, namely the selective oxidation of alcohols to aldehydes.