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The structure, dynamics, and thermal stability of the structurally similar 14-mer RNA hairpins uCACGg and cUUCGg are studied by using replica-exchange molecular dynamics simulations. The two RNA hairpins exhibited similar structures at room temperature, but the UUCG loop was found to be more flexible than the CACG loop.

We investigate energy transport through an [alpha]-aminoisobutyric acid-based [3.sub.10]-helix dissolved in chloroform in a combined experimental-theoretical approach. Vibrational energy is locally deposited at the N terminus of the helix by ultrafast internal conversion of a covalently attached, electronically excited, azobenzene moiety. Heat flow through the helix is detected with subpicosecond time resolution by employing vibrational probes as local thermometers at various distances from the heat source. The experiment is supplemented by detailed nonequilibrium molecular dynamics (MD) simulations of the process, revealing good qualitative agreement with experiment: Both theory and experiment exhibit an almost instantaneous temperature jump of the reporter units next to the heater which is attributed to the direct impact of the isomerizing azobenzene moiety. After this impact event, helix and azobenzene moiety appear to be thermally decoupled. The energy deposited in the helix thermalizes on a subpicosecond timescale and propagates along the helix in a diffusive-like process, accompanied by a significant loss into the solvent. However, in terms of quantitative numbers, theory and experiment differ. In particular, the MD simulation seems to overestimate the heat diffusion constant (2 [[Angstrom].sup.2] [ps.sup.-1] from the experiment) by a factor of five. energy dissipation | time-resolved IR spectroscopy | peptide helix | nonequilibrium molecular dynamics simulation

Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct assembly of amyloidogenic peptides we probe the dynamics of formation of [(A[[beta].sub.16-22]).sub.n] by adding a monomer to a preformed [(A[[beta].sub.16-22]).sub.n-1] (n = 4-6) oligomer in which the peptides are arranged in an antiparallel [beta]-sheet conformation. All atom molecular dynamics simulations in water and multiple long trajectories, for a cumulative time of 6.9 [micro]s, show that the oligomer grows by a two-stage dock-lock mechanism. The largest conformational change in the added disordered monomer occurs during the rapid ([approximately equal to] 50 ns) first dock stage in which the [beta]-strand content of the monomer increases substantially from a low initial value, in the second slow-lock phase, the monomer rearranges to form in register antiparallel structures. Surprisingly, the mobile structured oligomers undergo large conformational changes in order to accommodate the added monomer. The time needed to incorporate the monomer into the fluid-like oligomer grows even when n = 6, which suggests that the critical nucleus size must exceed six. Stable antiparallel structure formation exceeds hundreds of nanoseconds even though frequent interpeptide collisions occur at elevated monomer concentrations used in the simulations. The dock-lock mechanism should be a generic mechanism for growth of oligomers of amyloidogenic peptides.

Adopting trialanine as a paradigm of a small peptide, a comprehensive comparison of six popular force fields is presented, including the recent versions of AMBER, CHARMM, GROMOS, and OPLS models. For all force fields under consideration a 20ns long MD simulation is performed to study in detail the structure and conformational dynamics of the solvated peptide.

The fluorescence and resonance Raman emission of molecular systems undergoing ultrafast nonadiabatic isomerization is discussed. The validity of the approximation is studied by employing a two-mode, two-state model of photoisomerization of retinal.

A technique for the photoisomerization of retinal rhodopsin using a vibronically coupled electronic two-state system is described.

The time-resolved femtosecond spectroscopy in conjunction with nonequilibrium molecular dynamics (MD) simulations was used to study the energy transport in a short helical peptide in chloroform solution. A simple harmonic model of heat transport adopted on the bases of results showed that the heat diffusivity decreased significantly at temperatures initially reached by high-energy excitation.

The [phis], [psi] backbone angle distribution of small homopolymeric model peptides are examined by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. It is found that the alanine peptides [Ala.sub.n] exhibit the same conformational distribution.

The calculation of transient absorption spectra of cis-trans photoreactive system in the condensed phase is described theoretically. The formulation consists of a multidimensional model of nonadiabatic photoisomerization, a Redfield treatment of the environment within the secular approximation, and a doorway-window formulation to calculate transient pump-probe spectra.

A method for site-directed spin labeling of oligonucleotides with TPA and a precise 4-pulse electron double resonance (PELDOR) based nanometer distance ruler, in the range from 19 to 53 A for folded DNA/RNA in aqueous buffer solution, is presented.

The classical periodic orbits of an electron-transfer system are studied. Femtosecond time-resolved experiments on chemical and biophysical electron-transfer systems are conducted for this purpose and it is demonstrated that transient oscillations observed in electron-transfer femtosecond experiments may be explained in terms of a few classical trajectories.

The conformational structure and dynamics of trialanine in water are studied with the help of a molecular dynamics (MD) study. The MD study reveals that the conformational structures and dynamics show good overall agreement with experimental data.

The observation of subpicosecond fluctuations in the conformation of a small peptide in water is demonstrated. We use an experimental method that is specifically sensitive to conformational dynamics taking place on an ultrafast time scale. Complementary molecular-dynamics simulations confirm that the conformational fluctuations exhibit a subpicosecond component, the time scale and amplitude of which agree well with those derived from the experiment.