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.     

Eddy current and coupled landscapes for nonadiabatic and nonequilibrium complex system dynamics

Physical and biological systems are often involved with coupled processes of different time scales. In the system with electronic and atomic motions, for example, the interplay between the atomic motion along the same energy landscape and the electronic hopping between different landscapes is critical: the system behavior largely depends on whether the intralandscape motion is slower (adiabatic) or faster (nonadiabatic) than the interlandscape hopping. For general nonequilibrium dynamics where Hamiltonian or energy function is unknown a priori, the challenge is how to extend the concepts of the intra- and interlandscape dynamics. In this paper we establish a theoretical framework for describing global nonequilibrium and nonadiabatic complex system dynamics by transforming the coupled landscapes into a single landscape but with additional dimensions. On this single landscape, dynamics is driven by gradient of the potential landscape, which is closely related to the steady-state probability distribution of the enlarged dimensions, and the probability flux, which has a curl nature. Through an example of a self-regulating gene circuit, we show that the curl flux has dramatic effects on gene regulatory dynamics. The curl flux and landscape framework developed here are easy to visualize and can be used to guide further investigation of physical and biological nonequilibrium systems.     

Spectroscopic elucidation of uncoupled transition energies in the major photosynthetic light-harvesting complex,LHCII

Electrostatic couplings between chromophores in photosynthetic pigment–protein complexes, and interactions of pigments with the surrounding protein environment, produce a complicated energy landscape of delocalized excited states. The resultant electronic structure absorbs light and gives rise to energy transfer steps that direct the excitation toward a site of charge separation with near unity quantum efficiency. Knowledge of the transition energies of the uncoupled chromophores is required to describe how the wave functions of the individual pigments combine to form this manifold of delocalized excited states that effectively harvests light energy. In an investigation of the major light-harvesting complex of photosystem II (LHCII), we develop a method based on polarized 2D electronic spectroscopy to experimentally access the energies of the S₀–S₁ transitions in the chromophore site basis. Rotating the linear polarization of the incident laser pulses reveals previously hidden off-diagonal features. We exploit the polarization dependence of energy transfer peaks to find the angles between the excited state transition dipole moments. We show that these angles provide a spectroscopic method to directly inform on the relationship between the delocalized excitons and the individual chlorophylls through the site energies of the uncoupled chromophores.     

Evidence for a spontaneous gapped state in ultraclean bilayer graphene

At the charge neutrality point, bilayer graphene (BLG) is strongly susceptible to electronic interactions and is expected to undergo a phase transition to a state with spontaneously broken symmetries. By systematically investigating a large number of single-and double-gated BLG devices, we observe a bimodal distribution of minimum conductivities at the charge neutrality point. Although σ_min is often approximately 2–3 e²/h (where e is the electron charge and h is Planck’s constant), it is several orders of magnitude smaller in BLG devices that have both high mobility and low extrinsic doping. The insulating state in the latter samples appears below a transition temperature T_c of approximately 5 K and has a T = 0 energy gap of approximately 3 meV. Transitions between these different states can be tuned by adjusting disorder or carrier density.     

Investigation of Photoexcitation Energy Impact on Electron Mobility in Single Crystalline CdTe

The exceptional electronic properties of cadmium telluride (CdTe) allow the material to be used in a wide range of high energy radiation detection applications. Understanding the mechanisms of local carrier scattering is of fundamental importance to understand the charge transport in the material. Here, we investigate the effect of photoexcitation on electron transport properties in chlorine doped single crystalline cadmium telluride (SC-CdTe:Cl). For this purpose time of flight measurements were performed on SC-CdTe:Cl in order to study the electron drift mobility in the low injection regime. Measurements were made at the temperature intervals of 80 to 300 K, for an applied electric field between 270 and 1600 V/cm and for wavelengths of 532, 355 and 213 nm. We have found that the electron drift mobility was affected by the excitation energy for temperatures below 200 K. In addition, the measurements revealed that it is possible to determine impurity and shallow trap concentration by this method. The method proves to be extremely sensitive in measuring very low impurity levels and in identifying dominant scattering mechanisms.     

Two-dimensional electronic spectroscopy of the B800-B820 light-harvesting complex

Emerging nonlinear optical spectroscopies enable deeper insight into the intricate world of interactions and dynamics of complex molecular systems. 2D electronic spectroscopy appears to be especially well suited for studying multichromophoric complexes such as light-harvesting complexes of photosynthetic organisms as it allows direct observation of couplings between the pigments and charts dynamics of energy flow on a 2D frequency map. Here, we demonstrate that a single 2D experiment combined with self-consistent theoretical modeling can determine spectroscopic parameters dictating excitation energy dynamics in the bacterial B800-B820 light-harvesting complex, which contains 27 bacteriochlorophyll molecules. Ultrafast sub-50-fs dynamics dominated by coherent intraband processes and population transfer dynamics on a picosecond time scale were measured and modeled with one consistent set of parameters. Theoretical 2D spectra were calculated by using a Frenkel exciton model and modified F?rster/Redfield theory for the calculation of dynamics. They match the main features of experimental spectra at all population times well, implying that the energy level structure and transition dipole strengths are modeled correctly in addition to the energy transfer dynamics of the system.     

Solution of the coupled Einstein-Maxwell equations in oblate spheroidal coordinates

Using Ernst's theory of complex potentials, a solution of the coupled Einstein-Maxwell equations in oblate spheroidal coordinates is obtained for a source possessing mass, electric charge, and angular momentum. The density of the electromagnetic energy is evaluated. Explicit expressions are derived for the components of the Ricci tensor Rmunu, and of the electromagnetic energy momentum tensor Emunu, as well as for Enumu.     

Femtosecond coherent transient infrared spectroscopy of reaction centers from Rhodobacter sphaeroides.

Protein and cofactor vibrational dynamics associated with photoexcitation and charge separation in the photosynthetic reaction center were investigated with femto-second (300-400 fs) time-resolved infrared (1560-1960 cm-1) spectroscopy. The experiments are in the coherent transient limit where the quantum uncertainty principle governs the evolution of the protein vibrational changes. No significant protein relaxation accompanies charge separation, although the electric field resulting from charge separation modifies the polypeptide carbonyl spectra. The potential energy surfaces of the "special pair" P and the photoexcited singlet state P* and environmental perturbations on them are similar as judged from coherence transfer measurements. The vibrational dephasing time of P* modes in this region is 600 fs. A subpicosecond transient at 1665 cm-1 was found to have the kinetics expected for a sequential electron transfer process. Kinetic signatures of all other transient intermediates, P, P*, and P+, participating in the primary steps of photosynthesis were identified in the difference infrared spectra.     

Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching

The nucleocapsid protein (NC) of HIV type 1 is a nucleic acid chaperone that facilitates the rearrangement of nucleic acids into conformations containing the maximum number of complementary base pairs. We use an optical tweezers instrument to stretch single DNA molecules from the helix to coil state at room temperature in the presence of NC and a mutant form (SSHS NC) that lacks the two zinc finger structures present in NC. Although both NC and SSHS NC facilitate annealing of complementary strands through electrostatic attraction, only NC destabilizes the helical form of DNA and reduces the cooperativity of the helix-coil transition. In particular, we find that the helix-coil transition free energy at room temperature is significantly reduced in the presence of NC. Thus, upon NC binding, it is likely that thermodynamic fluctuations cause continuous melting and reannealing of base pairs so that DNA strands are able to rapidly sample configurations to find the lowest energy state. The reduced cooperativity allows these fluctuations to occur in the middle of complex double-stranded structures. The reduced stability and cooperativity, coupled with the electrostatic attraction generated by the high charge density of NC, is responsible for the nucleic acid chaperone activity of this protein.     

Damping Enhancement of Composite Panels by Inclusion of Shunted Piezoelectric Patches: A Wave-Based Modelling Approach

The waves propagating within complex smart structures are hereby computed by employing a wave and finite element method. The structures can be of arbitrary layering and of complex geometric characteristics as long as they exhibit two-dimensional periodicity. The piezoelectric coupling phenomena are considered within the finite element formulation. The mass, stiffness and piezoelectric stiffness matrices of the modelled segment can be extracted using a conventional finite element code. The post-processing of these matrices involves the formulation of an eigenproblem whose solutions provide the phase velocities for each wave propagating within the structure and for any chosen direction of propagation. The model is then modified in order to account for a shunted piezoelectric patch connected to the composite structure. The impact of the energy dissipation induced by the shunted circuit on the total damping loss factor of the composite panel is then computed. The influence of the additional mass and stiffness provided by the attached piezoelectric devices on the wave propagation characteristics of the structure is also investigated.     

Helix formation via conformation diffusion search

The helix-coil transition kinetics of an alpha-helical peptide were investigated by time-resolved infrared spectroscopy coupled with laser-induced temperature-jump initiation method. Specific isotope labeling of the amide carbonyl groups with 13C at selected residues was used to obtain site-specific information. The relaxation kinetics following a temperature jump, obtained by probing the amide I' band of the peptide backbone, exhibit nonexponential behavior and are sensitive to both initial and final temperatures. These data are consistent with a conformation diffusion process on the folding energy landscape, in accord with a recent molecular dynamics simulation study.     

Ultrafast Transient Spectroscopy of Polymer/Fullerene Blends for Organic Photovoltaic Applications

We measured the picoseconds (ps) transient dynamics of photoexcitations in blends of regio-regular poly(3-hexyl-thiophene) (RR-P3HT) (donors-D) and fullerene (PCBM) (acceptor-A) in an unprecedented broad spectral range of 0.25 to 2.5 eV. In D-A blends with maximum domain separation, such as RR-P3HT/PCBM, with (1.2:1) weight ratio having solar cell power conversion efficiency of ~4%, we found that although the intrachain excitons in the polymer domains decay within ~10 ps, no charge polarons are generated at their expense up to ~1 ns. Instead, there is a build-up of charge-transfer (CT) excitons at the D-A interfaces having the same kinetics as the exciton decay. The CT excitons dissociate into separate polarons in the D and A domains at a later time (>1 ns). This “two-step” charge photogeneration process may be typical in organic bulk heterojunction cells. We also report the effect of adding spin 1/2 radicals, Galvinoxyl on the ultrafast photoexcitation dynamics in annealed films of RR-P3HT/PCBM blend. The addition of Galvinoxyl radicals to the blend reduces the geminate recombination rate of photogenerated CT excitons. In addition, the photoexcitation dynamics in a new D-A blend of RR-P3HT/Indene C60 trisadduct (ICTA) has been studied and compared with the dynamics in RR-P3HT/PCBM.     

Real-time mapping of electronic structure with single-shot two-dimensional electronic spectroscopy

Electronic structure and dynamics determine material properties and behavior. Important time scales for electronic dynamics range from attoseconds to milliseconds. Two-dimensional optical spectroscopy has proven an incisive tool to probe fast spatiotemporal electronic dynamics in complex multichromophoric systems. However, acquiring these spectra requires long point-by-point acquisitions that preclude observations on the millisecond and microsecond time scales. Here we demonstrate that imaging temporally encoded information within a homogeneous sample allows mapping of the evolution of the electronic Hamiltonian with femtosecond temporal resolution in a single-laser-shot, providing real-time maps of electronic coupling. This method, which we call GRadient-Assisted Photon Echo spectroscopy (GRAPE), eliminates phase errors deleterious to Fourier spectroscopies while reducing the acquisition time by orders of magnitude using only conventional optical components. In analogy to MRI in which magnetic field gradients are used to create spatial correlation maps, GRAPE spectroscopy takes advantage of a similar type of spatial encoding to construct electronic correlation maps. Unlike magnetic resonance, however, this spatial encoding of the nonlinear polarization along the excitation frequency axis of the two-dimensional spectrum results in no loss in signal while simultaneously reducing overall noise. Correlating the energy transfer events and electronic coupling occurring in tens of femtoseconds with slow dynamics on the subsecond time scale is fundamentally important in photobiology, solar energy research, nonlinear spectroscopy, and optoelectronic device characterization.     

Regulating energy transfer of excited carriers and the case for excitation-induced hydrogen dissociation on hydrogenated graphene

Understanding and controlling of excited carrier dynamics is of fundamental and practical importance, particularly in photochemistry and solar energy applications. However, theory of energy relaxation of excited carriers is still in its early stage. Here, using ab initio molecular dynamics (MD) coupled with time-dependent density functional theory, we show a coverage-dependent energy transfer of photoexcited carriers in hydrogenated graphene, giving rise to distinctively different ion dynamics. Graphene with sparsely populated H is difficult to dissociate due to inefficient transfer of the excitation energy into kinetic energy of the H. In contrast, H can easily desorb from fully hydrogenated graphane. The key is to bring down the H antibonding state to the conduction band minimum as the band gap increases. These results can be contrasted to those of standard ground-state MD that predict H in the sparse case should be much less stable than that in fully hydrogenated graphane. Our findings thus signify the importance of carrying out explicit electronic dynamics in excited-state simulations.     

A note on the ground state energy of an assembly of interacting electrons

The ground state energy of an assembly of charged particles of density ρ imbedded in a continuum of charge of the other sign in an electrically neutral system is considered. Asymptotic formulae for the ground state energy of such systems are known in the high- and low-density regimes. An interpolation formula covering the entire density range is derived using the method of two-point Padé approximants. A phase transition from an electron lettice to an electron gas seems to occur at r₃ 14, r₃ being the radius of a sphere which, on the average, contains a single charge, in units of the Bohr radius of the electron in a hydrogen atom.     

UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases

Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)₄, and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.     

Charge Transport Characteristics of Molecular Electronic Junctions Studied by Transition Voltage Spectroscopy

The field of molecular electronics is prompted by tremendous opportunities for using a single-molecule and molecular monolayers as active components in integrated circuits. Until now, a wide range of molecular devices exhibiting characteristic functions, such as diodes, transistors, switches, and memory, have been demonstrated. However, a full understanding of the crucial factors that affect charge transport through molecular electronic junctions should yet be accomplished. Remarkably, recent advances in transition voltage spectroscopy (TVS) elucidate that it can provide key quantities for probing the transport characteristics of the junctions, including, for example, the position of the frontier molecular orbital energy relative to the electrode Fermi level and the strength of the molecule–electrode interactions. These parameters are known to be highly associated with charge transport behaviors in molecular systems and can then be used in the design of molecule-based devices with rationally tuned electronic properties. This article highlights the fundamental principle of TVS and then demonstrates its major applications to study the charge transport properties of molecular electronic junctions.     

Paired moving charges in mitochondrial energy coupling. II. Universality of the principles for energy coupling in biological systems.

The thesis is developed that an acceptable model of biological energy coupling must have universal application. The paired moving charge model of mitochondrial energy coupling is examined from the standpoint of this thesis. Fundamental to this model is the notion that energy coupling involves interaction between paired uncompensated charged species in two vectorially aligned and spatially separated reaction centers. The two charge-separating devices are assumed to be the electron transfer chain (in chloroplast and mitochondria) and intrinsic ionophores (in all transducing organelles and kinases). The universality of the ionophore principle becomes then the crucial test of the validity of the paired moving charge model. The multiple facets of ionophore-mediated couples processes are explored, e.g., coupled hydrolysis of ATP, hormonal control of ion movements, and active transport.