Chemical Physics

Proton transfer rates and mechanisms are studied in mesoscopic, liquid-state, molecular clusters. The proton transfer occurs in a proton-ion 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 the surface of the cluster or one layer of solvent molecules inside the surface. The proton transfer occurs as the complex undergoes orientational fluctuations on the cluster surface or penetrates one solvent layer into the cluster leading to solvent configurations that favor the transfer. For smaller clusters the complex resides mostly on the surface of the cluster and proton transfer is observed only when the complex penetrates the cluster and solvent configurations that favor the proton transfer are achieved. Quantitative information on the cluster reaction rate constants is also presented.

A closed form of the electrostatic potential of a homogeneously charged cube is derived by integration. The exact result is compared with multipole expansions for the exterior and interior of the cube. The electrostatic potential of a homogeneously charged square in two-dimensional electrostatics is also determined.

The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistical significant way. By performing Fourier transforms on the random walks one obtains additional evidence for non-randomness of the distributions. We have also analyzed results from a synthetic model containing only two amino-acid types, hydrophobic and hydrophilic. With reasonable criteria on good folding properties in terms of thermodynamical and kinetic behavior, sequences that fold well are isolated. Performing the same statistical analysis on the sequences that fold well indicates similar deviations from randomness as for the functional proteins. The deviations from randomness can be interpreted as originating from anticorrelations in terms of an Ising spin model for the hydrophobicities. Our results, which differ from previous investigations using other methods, might have impact on how permissive with respect to sequence specificity the protein folding process is -- only sequences with non-random hydrophobicity distributions fold well. Other distributions give rise to energy landscapes with poor folding properties and hence did not survive the evolution.

We present a barrier potential with bound states that is exactly solvable and determine the eigenfunctions and eigenvalues of the Hamiltonian. The equilibrium density matrix of a particle moving at temperature T in this nonlinear barrier potential field is determined. The exact density matrix is compared with the result of the path integral approach in the semiclassical approximation. For opaque barriers the simple semiclassical approximation is found to be sufficient at high temperatures while at low temperatures the fluctuation paths may have a caustic depending on temperature and endpoints. Near the caustics the divergence of the simple semiclassical approximation of the density matrix is removed by a nonlinear fluctuation potential. For opaque barriers the improved semiclassical approximation is again in agreement with the exact result. In particular, bound states and the form of resonance states are described accurately by the semiclassical approach.

The dynamical properties of exciton transfer coupled to polarization vibrations in a two site system are investigated in detail. A fixed point analysis of the full system of Bloch - oscillator equations representing the coupled excitonic - vibronic flow is performed. For overcritical polarization a bifurcation converting the stable bonding ground state to a hyperbolic unstable state which is basic to the dynamical properties of the model is obtained. The phase space of the system is generally of a mixed type: Above bifurcation chaos develops starting from the region of the hyperbolic state and spreading with increasing energy over the Bloch sphere leaving only islands of regular dynamics. The behaviour of the polarization oscillator accordingly changes from regular to chaotic.

An extension of the fermionic particle--particle propagator is presented, that possesses similar algebraic properties to the single--particle Green's function. In particular, this extended two--particle Green's function satisfies Dyson's equation and its self energy has the same analytic structure as the the self energy of the single--particle Green's function. For the case of a system interacting by one--particle potentials only, the two--particle self energy takes on a particularly simple form, just like the common self energy does. The new two--particle self energy also serves as a well behaved optical potential for the elastic scattering of a two--particle projectile by a many--body target. Due to its analytic structure, the two--particle self energy avoids divergences that appear with effective potentials derived by other means.

Using a Hubbard-Stratonovich transformation coupled with Fourier path integral methods, expressions are derived for the numerical evaluation of the microcanonical density of states for quantum particles obeying Boltzmann statistics. A numerical algorithmis suggested to evaluate the quantum density of states and illustrated on a one-dimensional model system.

We propose a novel method to measure the fractal dimension of a submonolayer metal adatom system grown under conditions of limited diffusivity on a surface. The method is based on measuring the specular peak attenuation of He atoms scattered from the surface, as a function of incidence energy. The (Minkowski) fractal dimension thus obtained is that of contours of constant electron density of the adatom system. Simulation results are presented, based on experimental data. A coverage dependent fractal dimension is found from a two-decade wide scaling regime.

Despite the seminal connection between classical multiply-periodic motion and Heisenberg matrix mechanics and the massive amount of work done on the associated problem of semiclassical (EBK) quantization of bound states, we show that there are, nevertheless, a number of previously unexploited aspects of this relationship that bear on the quantum-classical correspondence. In particular, we emphasize a quantum variational principle that implies the classical variational principle for invariant tori. We also expose the more indirect connection between commutation relations and quantization of action variables. With the help of several standard models with one or two degrees of freedom, we then illustrate how the methods of Heisenberg matrix mechanics described in this paper may be used to obtain quantum solutions with a modest increase in effort compared to semiclassical calculations. We also describe and apply a method for obtaining leading quantum corrections to EBK results. Finally, we suggest several new or modified applications of EBK quantization.

The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation, that is, to the energy landscape. The statistical energy landscape approach explains when and why unique behaviors, such as specific folding pathways, occur in some proteins and more generally explains the distinction between folding processes common to all sequences and those peculiar to individual sequences. This approach also gives new, quantitative insights into the interpretation of experiments and simulations of protein folding thermodynamics and kinetics. Specifically, the picture provides simple explanations for folding as a two-state first-order phase transition, for the origin of metastable collapsed unfolded states and for the curved Arrhenius plots observed in both laboratory experiments and discrete lattice simulations. The relation of these quantitative ideas to folding pathways, to uni-exponential {\em vs.} multi-exponential behavior in protein folding experiments and to the effect of mutations on folding is also discussed. The success of energy landscape ideas in protein structure prediction is also described. The use of the energy landscape approach for analyzing data is illustrated with a quantitative analysis of some recent simulations, and a qualitative analysis of experiments on the folding of three proteins. The work unifies several previously proposed ideas concerning the mechanism protein folding and delimits the regions of validity of these ideas under different thermodynamic conditions.