Biomedical subjects

Oleg V Prezhdo

Publications and source records attributed to Oleg V Prezhdo.

16 recordsLinked to original sources

PubMed2007

Theoretical studies of photoinduced electron transfer in dye-sensitized TiO2.

This review describes recent research into the properties of the chromophore-TiO2 interface that forms the basis for photoinduced charge separation in dye-sensitized semiconductor solar cells. It focuses particularly on an atomistic picture of the electron-injection dynamics. The interface offers an excellent case study, pertinent as well to a variety of other photovoltaic systems, photo- and electrochemistry, molecular electronics, analytical detection, photography, and quantum confinement devices. The differences between chemists' and physicists' models for describing molecules and bulk materials, respectively, create challenges for the characterization of interfaces that include both of these components. We give an overall picture of the interface by starting with a description of the properties of the chromophores and semiconductor separately, and then by discussing the coupled system, including the chromophore-semiconductor binding, electronic structure, and electron-injection dynamics. Explicit time-dependent modeling is particularly valuable for an understanding of the ultrafast electron injection because it shows a variety of individual injection events with well-defined dynamical features that cannot be made apparent by an average reaction-rate description.

Journal Article↗

PubMed2006

Force-induced deformations and stability of biological bonds.

A deformation model of the forced-induced dissociation of biological bonds is developed. A simple illustration shows that protein deformations can change the receptor-ligand interaction linearly with applied force at small forces, either increasing or decreasing the bond stability, and that a minor external work can lead to notable changes in the interaction energy. The deformation-induced increase of bond stability is illustrated with the remarkable catch-bond phenomenon in P and L selections. Additionally, the model rationalizes the frequently seen disparity between the bond dissociation rates of many free complexes and the zero-force asymptotic rates measured by force spectroscopy.

Binding Sites↗

PubMed2006

A quantum-classical bracket that satisfies the Jacobi identity.

A quantum-classical bracket is proposed and is shown to satisfy the Jacobi identity, in contrast to previous definitions that obey this property only up to higher order terms in the Planck constant variant Planck's over 2pi. The Jacobi identity is required of a true Lie bracket and ensures that the Lie bracket of constants of motion is also a constant of motion. An explicit calculation of the Jacobi identity highlights the difference between the proposed and traditional definitions. A further example illustrates that the proposed bracket generates a more consistent quantum-classical dynamics than the traditional bracket. The traditional quantum-classical dynamics in the Henon-Heiles system diverges due to higher order variant Planck's over 2pi terms. The divergence is eliminated with the proposed bracket.

Journal Article↗

PubMed2006

Dissociation of biological catch-bond by periodic perturbation.

The analysis of the P-selectin/PSGL-1 catch-slip bond that is periodically driven by a detaching force predicts that in the frequency range on the order of 1 s(-1) the bond lifetime undergoes significant changes with respect to both frequency and amplitude of the force. The result indicates how variations in the heart rate could have a substantial effect on leukocyte and lymphoid cell transport and adhesion to endothelial cells and platelets during inflammatory processes.

Animals↗

PubMed2006

Time-domain ab initio simulation of electron and hole relaxation dynamics in a single-wall semiconducting carbon nanotube.

The electron and hole relaxation in the (7, 0) zigzag carbon nanotube is simulated in time domain using a surface-hopping Kohn-Sham density functional theory. Following a photoexcitation between the second van Hove singularities, the electrons and holes decay to the Fermi level on characteristic subpicosecond time scales. Surprisingly, despite a lower density of states, the electrons relax faster than the holes. The relaxation is primarily mediated by the high-frequency longitudinal optical (LO) phonons. Hole dynamics are more complex than the electron dynamics: in addition to the LO phonons, holes couple to lower frequency breathing modes and decay over multiple time scales.

Journal Article↗

PubMed2006

Ultrafast vibrationally-induced dephasing of electronic excitations in PbSe quantum dots.

Vibrationally induced pure-dephasing of electronic states in PbSe quantum dots (QDs) at room temperature is investigated using two independent theoretical approaches based on the optical response function and semiclassical formalisms. Both approaches predict dephasing times of around 10 fs and reproduce the recently measured homogeneous linewidths of optical absorption well. Because dephasing slows down with increasing cluster size, the dephasing times calculated for the small clusters correspond to the lower end of the experimental data. The dephasing is almost independent of the electronic excitation energy and occurs faster for biexcitons than single excitons. The dephasing time is roughly proportional to the square root of the mass of the lighter atom (Se), suggesting that dephasing should be faster in PbS and slower in PbTe relative to PbSe. Core atoms produce stronger dephasing than surface atoms. In the collective description, pure-dephasing occurs via low-frequency acoustic modes, in support of the elastic QD model of dephasing. Because the electron-phonon coupling in PbSe QDs is relatively weak compared to other semiconductor nanocrystals, fast vibrationally induced dephasing can be expected in semiconductor QDs in general.

Computer Simulation↗

PubMed2005

Trajectory surface hopping in the time-dependent Kohn-Sham approach for electron-nuclear dynamics.

The mean-field treatment of electron-nuclear interaction results in many qualitative breakdowns in the time-dependent Kohn-Sham (TDKS) density functional theory. Examples include current-induced heating in nanoelectronics, charge dynamics in quantum dots and carbon nanotubes, and relaxation of biological chromophores. The problem is resolved by the trajectory surface-hopping TDKS approach, which is illustrated by the photoinduced electron injection from a molecular chromophore into TiO2, and the excited-state relaxation of the green fluorescent protein chromophore.

Journal Article↗

PubMed2005

Nonadiabatic molecular dynamics study of electron transfer from alizarin to the hydrated Ti4+ ion.

Ab initio real-time nonadiabatic (NA) molecular dynamics (MD) simulations are performed in order to investigate the photoinduced electron transfer (ET) from alizarin to the hydrated Ti4+ ion and compare it with the ET into bulk TiO2 that forms the basis of the Grätzel type solar cell. The experimental data and electronic structure calculations indicate that the photoexcitation spectra of alizarin attached to either bulk TiO2 or the Ti4+ ion in solution are very similar. In contrast, the NAMD simulations at ambient temperature predict marked differences between the ET dynamics that follow the photoexcitation in the two systems. The simulation of ET between alizarin and the TiO2 surface shows predominantly adiabatic transfer that occurs within 8 fs (Duncan et al. J. Am. Chem. Soc. 2005, 127, 7941), in agreement with the time-resolved experimental data. The simulation of alizarin attached to the hydrated Ti4+ ion reported presently predicts that the ET does occur, but on a slower 30 fs time scale, with a substantially reduced amplitude and by a predominantly NA mechanism. The differences are attributed to the disparity in the acceptor states of bulk TiO2 and the Ti4+ ion in solution. It is shown that the predicted alizarin-Ti4+ ET dynamics can be verified experimentally.

Journal Article↗

PubMed2005

Distinctive features of the biological catch bond in the jump-ramp force regime predicted by the two-pathway model.

The receptor-ligand unbinding in the biological catch bond is analyzed within a simple model that comprises a single bound state and two unbinding pathways. This model is investigated in detail for the jump-ramp force regime, where the pulling force quickly jumps to a finite value and then is ramped linearly with time. Two qualitative criteria are identified that distinguish the catch bond from the slip bond. First, the rupture force probability density of the catch-bond exhibits a maximum-minimum pair, which develops at finite forces. In contrast, the slip bond produces a maximum that first appears at zero force. Second, the catch bond can be identified over a wide range of ramp rates by high rupture probabilities at low forces relative to the probability at the maximum, in contrast to the slip bond, where the probability at the maximum always corresponds to the most likely rupture force. Both distinctive features of the catch bond are masked by large jump forces, indicating that the catch bond is best identified in experiments with moderate loading rates and small jump forces. The catch-bond lifetime in the constant force regime is related to the probability density in the jump-ramp regime, allowing one to determine the bond lifetime for a constant force by measuring the initial probability density in the jump-ramp experiments with different jump forces and a fixed ramp rate. The key analytic results are illustrated with the P -selectin/P-selectin glucoprotein ligand-1 bond.

Biophysics↗

PubMed2005

Second-order quantized Hamilton dynamics coupled to classical heat bath.

Starting with a quantum Langevin equation describing in the Heisenberg representation a quantum system coupled to a quantum bath, the Markov approximation and, further, the closure approximation are applied to derive a semiclassical Langevin equation for the second-order quantized Hamilton dynamics (QHD) coupled to a classical bath. The expectation values of the system operators are decomposed into products of the first and second moments of the position and momentum operators that incorporate zero-point energy and moderate tunneling effects. The random force and friction as well as the system-bath coupling are decomposed to the lowest classical level. The resulting Langevin equation describing QHD-2 coupled to classical bath is analyzed and applied to free particle, harmonic oscillator, and the Morse potential representing the OH stretch of the SPC-flexible water model.

Journal Article↗

PubMed2005

The two-pathway model for the catch-slip transition in biological adhesion.

Some recently studied biological noncovalent bonds have shown increased lifetime when stretched by mechanical force. In each case these counterintuitive "catch-bonds" have transitioned into ordinary "slip-bonds" that become increasingly shorter lived as the tensile force on the bond is further increased. We describe analytically how these results are supported by a physical model whereby the ligand escapes the receptor binding site via two alternative routes, a catch-pathway that is opposed by the applied force and a slip-pathway that is promoted by force. The model predicts under what conditions and at what critical force the catch-to-slip transition would be observed, as well as the degree to which the bond lifetime is enhanced at the critical force. The model is applied to four experimentally studied systems taken from the literature, involving the binding of P- and L-selectins to sialyl Lewis(X) oligosaccharide-containing ligands. Good quantitative fit to the experimental data is obtained, both for experiments with a constant force and for experiments where the force increases linearly with time.

Adhesiveness↗

PubMed2005

Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection across the alizarin-TiO2 interface.

The observed 6-fs photoinduced electron transfer (ET) from the alizarin chromophore into the TiO2 surface is investigated by ab initio nonadiabatic (NA) molecular dynamics in real time and at the atomistic level of detail. The system derives from the dye-sensitized semiconductor Grätzel cell and addresses the problems of an organic/inorganic interface that are commonly encountered in photovoltaics, photochemistry, and molecular electronics. In contrast to the typical Grätzel cell systems, where molecular donors are in resonance with a high density of semiconductor acceptor states, TiO2 sensitized with alizarin presents a novel case in which the molecular photoexcited state is at the edge of the conduction band (CB). The high level ab initio analysis of the optical absorption spectrum supports this observation. Thermal fluctuations of atomic coordinates are particularly important both in generating a nonuniform distribution of photoexcited states and in driving the ET process. The NA simulation resolves the controversy regarding the origin of the ultrafast ET by showing that although ultrafast transfer is possible with the NA mechanism, it proceeds mostly adiabatically in the alizarin-TiO2 system. The simulation indicates that the electron is injected into a localized surface state within 8 fs and spreads into the bulk on a 100-fs or longer time scale. The molecular architecture seen in the alizarin-TiO2 system permits efficient electron injection into the edge of the CB by an adiabatic mechanism without the energy loss associated with injection high into the CB by a NA process.

Journal Article↗

PubMed2005

Electronic structure and spectra of catechol and alizarin in the gas phase and attached to titanium.

Ab initio electronic structure calculations elucidate the dramatic differences observed in the electronic spectra of the catechol and alizarin molecules upon binding to titanium. Catechol and alizarin are similar chromophores with analogous electronic spectra in the free state. Binding alizarin to titanium red-shifts the spectrum. The binding of catechol to titanium produces a new optically active transition, at the same time preserving the features of the free catechol spectrum. By examining the details of the calculations, we can rationalize the spectral differences in the catechol and alizarin systems by the positioning of the catechol and alizarin pi molecular orbitals relative to the conduction band of TiO(2).

Journal Article↗

PubMed2004

Macroscopic order and electro-optic response of dipolar chromophore-polymer materials.

This Minireview considers the key factors that govern the organization of macroscopic polarization in nonlinear optical systems obtained by electric poling of organic dipolar chromophores dissolved in polymer matrices. The macroscopic electric polarization depends on the thermodynamic state of the dipole system. The dependence of the paraelectric and antiferroelectric states of dipolar chromophores on the chromophore concentration and the strength of the poling field is discussed. Phase transitions between the para- and antiferroelectric states are investigated within the limits of the Ising and isotropic models for the chromophore dipoles and are considered for varying chromophore concentration, poling field strength, and macroscopic shape of the sample used for poling. The macroscopic polarization and electro-optic coefficient of the material change drastically upon phase transition. The theories are compared with the experimental data on the electro-optic coefficient dependence on the chromophore concentration. The isotropic dipole model shows excellent agreement with experiment for the chromophore systems most commonly used in nonlinear optics.

Journal Article↗

PubMed2004

A canonical averaging in the second-order quantized Hamilton dynamics.

Quantized Hamilton dynamics (QHD) is a simple and elegant extension of classical Hamilton dynamics that accurately includes zero-point energy, tunneling, dephasing, and other quantum effects. Formulated as a hierarchy of approximations to exact quantum dynamics in the Heisenberg formulation, QHD has been used to study evolution of observables subject to a single initial condition. In present, we develop a practical solution for generating canonical ensembles in the second-order QHD for position and momentum operators, which can be mapped onto classical phase space in doubled dimensionality and which in certain limits is equivalent to thawed Gaussian. We define a thermal distribution in the space of the QHD-2 variables and show that the standard beta=1/kT relationship becomes beta'=2/kT in the high temperature limit due to an overcounting of states in the extended phase space, and a more complicated function at low temperatures. The QHD thermal distribution is used to compute total energy, kinetic energy, heat capacity, and other canonical averages for a series of quartic potentials, showing good agreement with the quantum results.

Journal Article↗

PubMed2004

Electron-nuclear correlations for photo-induced dynamics in molecular dimers.

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by the dynamic reorganization of inter- and intra- molecular nuclear configuration modeled by a quantized nuclear degree of freedom. The dynamics of the electronic population and nuclear coherence is analyzed by solving the chain of coupled differential equations for population inversion, electron-vibrational correlation, etc. Intriguing results are obtained in the approximation of a small change of the nuclear equilibrium upon photoexcitation. In the limiting case of resonance between the electronic energy gap and the frequency of the nuclear mode these results are justified by comparison to the exactly solvable Jaynes-Cummings model. It is found that the photoinduced processes in the model dimer are arranged according to their time scales: (i) Fast scale of nuclear motion, (ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electron-nuclear correlation, (iii) slow scale of electronic population approach to the quasi-equilibrium distribution, decay of electron-nuclear correlation, and decrease of the amplitude of mean coordinate oscillation. The latter processes are accompanied by a noticeable growth of the nuclear coordinate dispersion associated with the overall nuclear wave packet width. The demonstrated quantum relaxation features of the photoinduced vibronic dynamics in molecular dimers are obtained by a simple method, applicable to systems with many degrees of freedom.

Journal Article↗