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Biomedical subjects

Shaul Mukamel

Publications and source records attributed to Shaul Mukamel.

At least 19 recordsLinked to original sources
PubMed2006

Coherent control of cross-peaks in chirality-induced two-dimensional optical signals of excitons.

Polarization tuning of the interference of chirality-induced tensor components is used to simulate the suppression of diagonal peaks and amplification of cross peaks in femtosecond two-dimensional photon echo signals of excitons in a chiral porphyrin dimer. Superpositions of various tensor components which generate the optimized signals are constructed using a genetic learning algorithm. Exciton couplings and bath correlations may be extracted from these highly resolved signals.

Algorithms↗
PubMed2006

Two-dimensional vibrational optical probes for peptide fast folding investigation.

A simulation study shows that early protein folding events may be investigated by using a recently developed family of nonlinear infrared techniques that combine the high temporal and spatial resolution of multidimensional spectroscopy with the chirality-specific sensitivity of amide vibrations to structure. We demonstrate how the structural sensitivity of cross-peaks in two-dimensional correlation plots of chiral signals of an alpha helix and a beta hairpin may be used to clearly resolve structural and dynamical details undetectable by one-dimensional techniques (e.g. circular dichroism) and identify structures indistinguishable by NMR.

Computer Simulation↗
PubMed2006

Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory map.

The coherent nonlinear response of the entire amide line shapes of N-methyl acetamide to three infrared pulses is simulated using an electrostatic density functional theory map. Positive and negative cross peaks contain signatures of correlations between the fundamentals and the combination state. The amide I-A and I-III cross-peak line shapes indicate positive correlation and anticorrelation of frequency fluctuations, respectively. These can be ascribed to correlated hydrogen bonding at C[double bond]O and N-H sites. The amide I frequency is negatively correlated with the hydrogen bond on carbonyl C[double bond]O, whereas the amide A and III are negatively and positively correlated, respectively, with the hydrogen bond on amide N-H.

Acetamides↗
PubMed2006

Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy.

The stochastic Liouville equations are employed to investigate the combined signatures of chemical exchange (two-state jump) and spectral diffusion (coupling to an overdamped Brownian oscillator) in the coherent response of an anharmonic vibration to three femtosecond infrared pulses. Simulations reproduce the main features recently observed in the OD stretch of phenol in benzene.

Algorithms↗
PubMed2006

Optical coherence and theoretical study of the excitation dynamics of a highly symmetric cyclophane-linked oligophenylenevinylene dimer.

Optoelectronic properties of a polyphenylenevinylene-based oligomer and its paracylophane-linked dimer are studied using a variety of experimental and theoretical techniques. Despite the symmetrical structure and redshifted absorption of the dimer versus the monomer, an exciton picture is not the most appropriate. Electronic structure calculations establish changes in charge density upon optical excitation and show localized excitations that cannot be accounted for by a simple Frenkel exciton model. Visible frequency pump-probe anisotropy measurements suggest that the dimer should be considered as a three-level system with a fast, approximately 130 fs, internal conversion from the higher to lower energy excited electronic state. Signatures of nuclear relaxation processes are compared for electric field-resolved transient grating and two-dimensional photon echo spectra. These measurements reveal that nuclear relaxation occurs on similar time scales for the monomer and dimer. The connection between the spectral phase of four-wave mixing signals and the time dependent width of a nuclear wave packet is discussed. Semiempirical electronic structure and metropolis Monte Carlo calculations show that the dominant line broadening mechanisms for the monomer and dimer are associated with inter-ring torsional coordinates. Together, the theoretical calculations and electric field-resolved four-wave mixing experiments suggest that while the structure of dimer is more rigid than that of monomer, the difference in their rigidities is not sufficient to slow down excited state relaxation of dimer with respect to the monomer.

Journal Article↗
PubMed2006

Simulation of single molecule inelastic electron tunneling signals in paraphenylene-vinylene oligomers and distyrylbenzene[2.2]paracyclophanes.

Inelastic resonances in the electron tunneling spectra of several conjugated molecules are simulated using the nonequilibrium Greens function formalism. The vibrational modes that strongly couple to the electronic current are different from the infrared and Raman active modes. Spatially resolved inelastic electron tunneling (IET) intensities are predicted. The simulated IET intensities for a large distyrylbenzene paracyclophane molecule are in qualitative agreement with recent experimental results.

Journal Article↗
PubMed2006

Fluctuation theorems for quantum master equations.

A quantum fluctuation theorem for a driven quantum subsystem interacting with its environment is derived based solely on the assumption that its reduced density matrix obeys a closed evolution equation--i.e., a quantum master equation (QME). Quantum trajectories and their associated entropy, heat, and work appear naturally by transforming the QME to a time-dependent Liouville space basis that diagonalizes the instantaneous reduced density matrix of the subsystem. A quantum integral fluctuation theorem, a steady-state fluctuation theorem, and the Jarzynski relation are derived in a similar way as for classical stochastic dynamics.

Entropy↗
PubMed2006

Cooperative effects in photon statistics of molecular dimers with spectral diffusion.

The two-point fluorescence intensity correlation function g(2)t and the Mandel parameter Mt are calculated for a strongly pumped dimer of two-level molecules undergoing Gaussian-Markovian frequency fluctuations. The effects of detuning and saturation are examined. All fluctuation time scale regimes are explored using a continued fraction solution of the stochastic Liouville equation for the generating function. Bunching and antibunching are observed for slow and fast fluctuations, respectively. The short-time antibunching dip in g(2) and its variation with intermolecular coupling, the exciton annihilation rate, and laser detuning are studied.

Journal Article↗
PubMed2006

Coherence and correlations in multitime quantum measurements of stochastic quantum trajectories.

Quantum effects on multitime distributions and correlation functions of single objects, stemming from both the dynamics and repeated measurements, are calculated for a driven harmonic system using a superoperator generating functional formalism. Marked differences between multipoint observables associated with classical and quantum measurements are identified. The effects of quantum collapse and measurement resolution are discussed.

Journal Article↗
PubMed2006

Simulation of x-ray absorption near-edge spectra and x-ray fluorescence spectra of optically excited molecules.

The x-ray absorption near-edge spectra (XANES) and fluorescence spectra of molecules in the ground state and optically excited states are computed using time-dependent density functional theory and time-dependent Hartree-Fock theory. The calculated XANES spectra of optically excited methanol, benzonitrile, hydrogen sulphide, and titanium tetrachloride and the fluorescence spectra of optically excited methanol can be used to simulate ultrafast optical pump/x-ray probe experiments.

Journal Article↗
PubMed2006

Simulation protocols for coherent femtosecond vibrational spectra of peptides.

Two algorithms for simulating the response of peptides to sequences of IR pulses are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D(2)O. A fluctuating vibrational-exciton Hamiltonian for the amide I mode is constructed from molecular dynamics trajectories. Coupling with the environment is described using a density functional theory electrostatic map. The cumulant expansion of Gaussian fluctuation incorporates motional narrowing due to fast frequency fluctuations and is adequate for NMA and for isotopically labeled bands in large peptides. Real-space truncation of the scattering matrix of the nonlinear exciton equations significantly reduces the computational cost, making it particularly attractive for slow fluctuations in large globular proteins.

Chemistry, Physical↗
PubMed2006

Nonequilibrium superoperator GW equations.

Hedin's equations [Phys. Rev. 139, 796 (1965)] for the one-particle equilibrium Green's function of a many-electron system are generalized to nonequilibrium open systems using two fields that separately control the evolution of the bra and the ket of the density matrix. A closed hierarchy is derived for the Green's function, the self-energy, the screened potential, the polarization, and the vertex function, all expressed as Keldysh matrices in Liouville space.

Journal Article↗
PubMed2006

Chirality-induced signals in coherent multidimensional spectroscopy of excitons.

The nonlocal second- and third-order susceptibilities of an isotropic ensemble of aggregates are calculated by solving the nonlinear exciton equations which map the system into coupled anharmonic oscillators. Both electric and magnetic contributions are included using the minimal-coupling Hamiltonian. The various tensor components are evaluated to first order in the optical wave vector k. Additional structural information about the interchromophore distances, which is not accessible through zeroth-order contributions (the dipole approximation), is contained to the first order in k. New resonant second- and third-order signals predicted for chiral molecules provide multidimensional extensions of circular dichroism spectroscopy. Numerical simulations demonstrate the sensitivity of third-order signals to the secondary structural motiffs of peptides.

Circular Dichroism↗
PubMed2006

Coherent control of pump-probe signals of helical structures by adaptive pulse polarizations.

The simplification of the pump-probe spectrum of excitons by pure-phase-polarization pulse shaping is investigated by a simulation study. The state of light is manipulated by varying the phases of two perpendicular polarization components of the pump, holding its total spectral and temporal intensity profiles fixed. Genetic and iterative Fourier transform algorithms are used to search for pulse phase functions that optimize the ratio of the signal at two frequencies. New features are extracted from the congested pump-probe spectrum of a helical pentamer by selecting a combination of Liouville space pathways. Tensor components which dominate the optimized spectra are identified.

Journal Article↗
PubMed2006

Anomalous continuous-time random-walk spectral diffusion in coherent third-order optical response.

Recursive relations are derived for nonlinear optical response functions of a two-level chromophore with stochastic frequency fluctuations described by a continuous-time random walk. Stationary ensembles are constructed and signatures of anomalous relaxation in the photon echo signal are discussed for a two state jump modulation with a power law waiting time density function psi(t) approximately t(-alpha-1). Stretched exponential decay of the photon echo signal is predicted for 0<alpha<1 and power law asymptotics for 1<alpha<2.

Journal Article↗
PubMed2005

Electrostatic DFT map for the complete vibrational amide band of NMA.

An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.

Amides↗
PubMed2005

Multipoint correlation functions for continuous-time random walk models of anomalous diffusion.

Recursive relations are developed for computing the multipoint correlation functions of a particle undergoing a biased continuous-time random walk (CTRW) in an external potential. Two- and three-point correlation functions are calculated for waiting-time distributions with an anomalous power-law profile t(-alpha-1), 0 < alpha < 1, on intermediate time scales with a crossover to an exponential long time decay. Comparison of the CTRW with the Brownian harmonic oscillator model (Gaussian process) illustrates how higher-order correlation functions may be used to distinguish between dynamical models that have the same two-point correlation function.

Colloids↗