Biomedical subjects

S Mukamel

Publications and source records attributed to S Mukamel.

At least 19 recordsLinked to original sources

PubMed2001

Signatures of beta-peptide unfolding in two-dimensional vibrational echo spectroscopy: a simulation study.

An ensemble of exciton Hamiltonians for the amide-I band of the folded and unfolded states of a helical beta-heptapeptide is generated using a molecular dynamics (MD) simulation. The correlated fluctuations of its parameters and their signatures in two-dimensional (2D) vibrational echo spectroscopy are computed. This technique uses infrared pulse sequences to provide ultrafast snapshots of molecular structural fluctuations, in analogy with multidimensional NMR. The present study demonstrates that, by combining a method of calculating the vibrational Hamiltonian from MD snapshots and the nonlinear exciton equations (NEE), it may be possible to simulate realistic multidimensional IR spectra of chemically and biologically interesting systems.

Computer Simulation↗

PubMed2001

Exciton coherence and electron energy loss spectroscopy of conjugated molecules.

Signatures of the exciton coherence size, which controls the nonlinear optical response and luminescence of conjugated systems, in the electronic dynamic structure factor S(q,omega) are calculated. We find that for small molecules the momentum dependence of the lowest exciton resonance is purely geometric, reflecting the molecular size rather than a universal exciton size, as suggested recently. For long chains the q dependence is determined by the interplay of the exciton size and the bond-alternation length scales.

Journal Article↗

PubMed2000

Excitonic funneling in extended dendrimers with nonlinear and random potentials

The mean first passage time (MFPT) for photoexcitations diffusion in a funneling potential of artificial treelike light-harvesting antennas (phenylacetylene dendrimers with generation-dependent segment lengths) is computed. Effects of the nonlinearity of the realistic funneling potential and slow random solvent fluctuations considerably slow down the center-bound diffusion beyond a temperature-dependent optimal size. Diffusion on a disordered Cayley tree with a linear potential is investigated analytically. At low temperatures we predict a phase in which the MFPT is dominated by a few paths.

Journal Article↗

PubMed2000

Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations.

Femtosecond visible and infrared analogues of multiple-pulse nuclear magnetic resonance techniques provide novel snapshot probes into the structure and electronic and vibrational dynamics of complex molecular assemblies such as photosynthetic antennae, proteins, and hydrogen-bonded liquids. A classical-oscillator description of these spectroscopies in terms of interacting quasiparticles (rather than transitions among global eigenstates) is developed and sets the stage for designing new pulse sequences and inverting the multidimensional signals to yield molecular structures. Considerable computational advantages and a clear physical insight into the origin of the response and the relevant coherence sizes are provided by a real-space analysis of the underlying coherence-transfer pathways in Liouville space.

Journal Article↗

PubMed1999

Excitonic couplings and electronic coherence in bridged naphthalene dimers.

The electronic excitations of naphthalene and a family of bridged naphthalene dimers are calculated and analyzed by using the Collective Electronic Oscillator method combined with the oblique Lanczos algorithm. All experimentally observed trends in absorption profiles and radiative lifetimes are reproduced. Each electronic excitation is linked to the corresponding real-space transition density matrix, which represents the motions of electrons and holes created in the molecule by photon absorption. Two-dimensional plots of these matrices help visualize the degree of exciton localization and explain the dependence of the electronic interaction between chromophores on their separation.

Journal Article↗

PubMed1996