Mapping Hydration Dynamics around a β-Barrel Protein.

Windows or eyeglasses that darken in bright light are examples of nonlinear optical materials, in which the response of the medium, in this case the refractive index, changes dramatically with the light intensity. However, the response time, typically seconds, of these materials is too slow to be of practical use for electro-optic or all-optical switching processes. The combination of intense coherent radiation available from lasers together with newly developed photorefractive materials is providing nonlinear optical response times on ultrafast time scales. Such systems allow photons to be added, subtracted, mixed, and manipulated in ways impossible in our familiar low-light-intensity environment. The Reviews in this special issue of Science look at some of those developments in the field of nonlinear optics and the applications they are finding. To study the dynamics of an event too fast for our eyes to see, snapshots of the event are taken, pieced together, and then played back in slow motion. Cameras equipped with fast mechanical shutters allow us to view microsecond snippets of time. The detailed dynamics of chemical reactions or of electronic transitions in crystalline materials can be revealed in a similar manner by following processes with laser pulses on time scales of picoseconds (10−12 s) or femtoseconds (10−15 s). Steinmeyer et al. (p. [1507][1]) review the role of nonlinear optics in the generation of ultrafast laser pulses and focus on the role being played by direct laser oscillators. It is necessary in spectroscopy to tune in to the energy scale that is relevant to the particular system under study. However, lasers generally emit light at very precise and fixed wavelengths. Dunn and Ebrahimzadeh (p. [1513][2]) describe how high-quality monochromatic light can be generated with optical parametric oscillators in which the interaction between photons can be controlled. This approach achieves a flexibility in generating the output light that is not available to conventional lasers. The past decade has seen an explosion in communication technology. The continuing challenge is to transfer ever-larger amounts of information from one point to another at as high a rate as possible without losing any data in the process. One proposal to overcome the transfer rate limitation of semiconductors is to use all-optical networks. Today, thousands of kilometers of optical fibers encircle the globe. As more information is transferred down a fiber, however, nonlinearities become important and can actually limit the information capacity. As a light pulse propagates through a medium, it disperses or broadens, and repeater stations are needed periodically to prevent pulses from smearing into one another. However, with sufficiently high light intensity, the refractive index of the medium is locally increased and the light is confined to that region by total internal reflection. The light then traverses the medium without loss of intensity and is described as a spatial soliton. Stegeman and Segev (p. [1518][3]) review how such nonlinearities can be used to advantage in the generation and interaction of solitons in their role as information carriers, and Cotter et al. (p. [1523][4]) review the techniques required to implement processing of the optical signals at transfer rates in excess of 100 gigabits per second. A News story (p. [1502][5]) examines the promise of storing such torrents of data in holograms: durable optical inscriptions written in nonlinear optical materials. And two other News stories (pp. [1500][6] and [1504][7]) describe progress in other fields of optics: latticelike photonic crystals, which can trap or channel light; and adaptive optics technology, which helps telescopes undo the effects of atmospheric turbulence. [1]: /lookup/doi/10.1126/science.286.5444.1507 [2]: /lookup/doi/10.1126/science.286.5444.1513 [3]: /lookup/doi/10.1126/science.286.5444.1518 [4]: /lookup/doi/10.1126/science.286.5444.1523 [5]: /lookup/doi/10.1126/science.286.5444.1502 [6]: /lookup/doi/10.1126/science.286.5444.1500 [7]: /lookup/doi/10.1126/science.286.5444.1504

Rigidity, Secondary Structure, and the Universality of the Boson Peak in Proteins

Introducing NMR strategies to define water molecules that drive metal binding in a transcriptional regulator

Photosynthetic light-harvesting antennae direct energy collected from sunlight to reaction centers with remarkable efficiency and rapidity. Despite their common function, the pigment-protein complexes that make up antenna systems in different types of photosynthetic organisms exhibit a wide variety of structural forms. Some individual organisms express different types of complexes depending on growth conditions. For example, purple photosynthetic bacteria Rp. palustris preferentially synthesize light-harvesting complex 4 (LH4), a structural variant of the more common and widely studied LH2, when grown under low-light conditions. Here, we investigate the ultrafast dynamics and energy level structure of LH4 using two-dimensional (2D) electronic spectroscopy in combination with theoretical simulations. The experimental data reveal dynamics on two distinct time scales, consistent with coherent dephasing within approximately the first 100 fs, followed by relaxation of population into lower-energy states on a picosecond time scale. We observe excited state absorption (ESA) features marking the existence of high-energy dark states, which suggest that the strongest dipole-dipole coupling in the complex occurs between bacteriochlorophyll transition dipole moments in an in-line geometry. The results help to refine the current understanding of the pigment organization in the LH4 complex, for which a high-resolution crystal structure is not yet available.

Time-dependent Stokes shift (TDSS) responses in proteins and DNA exhibit a broad range of long time scales (>10 ps) that are not present in bulk aqueous solution. The physical interpretation of the long TDSS time scales in biomolecular systems is a matter of considerable debate because of the many different components present in the sample (water, biomolecule, counterions), which have highly correlated motions and intrinsically different abilities to adapt to local perturbations. Here we use molecular dynamics (MD) simulations to show that the surprisingly slow (∼10 ns) TDSS response of coumarin 102 (C102), a base pair replacement, reflects a distinct dynamical signature for DNA damage. When the C102 molecule is covalently incorporated into DNA, an abasic site is created on the strand opposite the C102 probe. The abasic sugar exhibits a reversible interchange between intra- and extrahelical conformations that are kinetically stable on a nanosecond time scale. This conformational change, only possible in damaged DNA, was found to be responsible for the long time scales in the measured TDSS response. For the first time, a TDSS measurement has been attributed to a specific biomolecular motion. This finding directly contradicts the prevailing notion that the TDSS response in biomolecular contexts is dominated by hydration dynamics. It also suggests that TDSS experiments can be used to study ultrafast biomolecular dynamics that are inaccessible to other techniques.

Field-dependent 35Cl spin relaxation rates have been measured in the micellar solution of C16TACl−D2O. The data are analyzed in terms of a fast hydration dynamics of the ion and a slower motion that consists of ion diffusion and micellar tumbling. This model provides a distinct motional correlation time of the Cl- ion from which it is concluded that, on the nanosecond time scale, the Cl- ion diffuses on the micellar surface close to its bulk diffusion speed. The hydration dynamics on the picosecond time scale differs from that in a dilute solution. These features are similar to that observed for Br- ions in the vicinity of aqueous micelles of C16TABr (Hedin, N.; Furo, I. J. Phys. Chem. B 1999, 103, 9640).

We report our direct study of complex protein dynamics in human thioredoxin by dissecting into elementary processes and determining their relevant time scales. By combining site-directed mutagenesis with femtosecond spectroscopy, we have distinguished four partly time-overlapped dynamical processes at the active site of thioredoxin. Using intrinsic tryptophan as a molecular probe and from mutation studies, we ascertained the negligible contribution to solvation by protein sidechains and observed that the hydration dynamics at the active site occur in 0.47-0.67 and 10.8-13.2 ps. With reduced and oxidized states, we determined the electron-transfer quenching dynamics between excited tryptophan and a nearby disulfide bond in 10-17.5 ps for three mutants. A robust dynamical process in 95-114 ps, present in both redox states and all mutants regardless of neighboring charged, polar, and hydrophobic residues around the probe, is attributed to the charge transfer reaction with its adjacent peptide bond. Site-directed mutations also revealed the electronic quenching dynamics by an aspartate residue at a hydrogen bond distance in 275-615 ps. The local rotational dynamics determined by the measurement of anisotropy changes with time unraveled a relatively rigid local configuration but implies that the protein fluctuates on the time scale of longer than nanoseconds. These results elucidate the temporal evolution of hydrating water motions, electron-transfer reactions, and local protein fluctuations at the active site, and show continuously synergistic dynamics of biological function over wide time scales.

The nonlinear saturation of crossed-beam energy transfer (CBET) for multispeckled laser beams crossing at arbitrary angles is examined using vector particle-in-cell simulations. CBET is found to saturate on fast (∼10s of picosecond) time scales involving ion trapping and excitation of oblique forward stimulated Raman scattering (FSRS). Ion trapping reduces wave damping and speckle interaction increases wave coherence length, together enhancing energy transfer; ion acoustic wave (IAW) breakup in the direction transverse to the wavenumber increases wave damping and contributes to CBET saturation. The seed beam can become unstable to oblique FSRS, which leads to beam deflection at a large angle and a frequency downshift (by the plasma frequency). FSRS saturates on fast ∼picosecond time scales by electron plasma wave self-focusing, leading to enhanced side-loss hot electrons with energy exceeding 300 keV. This may contribute to fuel preheat but FSRS can be mitigated by the presence of a density gradient. Such growth of FSRS contributes to the saturation of CBET. Scaling simulations show that CBET, as well as FSRS and hot electrons, increases with beam average intensity, beam diameter, and crossing area, but that CBET is limited by the excitation of FSRS and IAW breakups in addition to pump depletion. FSRS deflects the seed beam energy by greater than 40% of the incident beam energy and puts a few percent of the incident beam energy into hot electrons. FSRS limits the efficacy of CBET for symmetry tuning at late stages in the implosion and may account for a large portion of the “missing energy” in implosions that use gas-filled hohlraums.

This work shows that detectable terahertz (THz) frequency radiation can be emitted when a wurtzite-structure crystal transforms to a rocksalt structure under shock compression on picosecond time scales. Information about the atomic-scale transformation pathway is contained in the sign of the emitted THz electric field and information about the kinetics is contained in the time dependence. This phenomenon provides an avenue to experimental measurement of microscopic transformation pathways in crystals on the shortest (picosecond) time scales.

Starting with a formally exact diagrammatic kinetic theory for the equilibrium correlation functions of particle density and current fluctuations for a monatomic liquid, we develop a theory for high density liquids whose interatomic potential is continuous and has a strongly repulsive short ranged part. We assume that interparticle collisions via this short ranged part of the potential are sufficient to randomize the velocities of the particles on a very small time scale compared with the fundamental time scale defined as the particle diameter divided by the mean thermal velocity. When this is the case, the graphical theory suggests that both the particle current correlation functions and the memory function of the particle density correlation function evolve on two distinct time scales, the very short time scale just mentioned and another that is much longer than the fundamental time scale. The diagrams that describe the motion on each of these time scales are identified. When the two time scales are very different, a dramatic simplification of the diagrammatic theory at long times takes place. We identify an irreducible memory function and a more basic function, which we call the irreducible memory kernel. This latter function evolves on the longer time scale only and determines the time dependence of the density and current correlation functions of interest at long times. In Paper II, a simple one-loop approximation for the irreducible memory kernel is used to calculate correlation functions for a Lennard-Jones fluid at high density and a variety of temperatures.

Heatmanagement is crucial in the design of nanoscale devices asthe operating temperature determines their efficiency and lifetime.Past experimental and theoretical works exploring nanoscale heat transportin semiconductors addressed known deviations from Fourier’slaw modeling by including effective parameters, suchas a size-dependent thermal conductivity. However, recent experimentshave qualitatively shown behavior that cannot be modeled in this way.Here, we combine advanced experiment and theory to show that the coolingof 1D- and 2D-confined nanoscale hot spots on silicon can be describedusing a general hydrodynamic heat transport model, contrary to previousunderstanding of heat flow in bulk silicon. We use a comprehensiveset of extreme ultraviolet scatterometry measurements of nondiffusivetransport from transiently heated nanolines and nanodots to validateand generalize our ab initio model, that does notneed any geometry-dependent fitting parameters. This allows us touncover the existence of two distinct time scales and heat transportmechanisms: an interface resistance regime that dominates on shorttime scales and a hydrodynamic-like phonon transport regime that dominateson longer time scales. Moreover, our model can predict the full thermomechanicalresponse on nanometer length scales and picosecond time scales forarbitrary geometries, providing an advanced practical tool for thermalmanagement of nanoscale technologies. Furthermore, we derive analyticalexpressions for the transport time scales, valid for a subset of geometries,supplying a route for optimizing heat dissipation.

The Si−H bond activation reactions by group VIIB, d6 organometallic compounds η5-CpM(CO)3 (M = Mn, Re; Cp = C5 H5) were studied in neat triethylsilane under ambient conditions. Utilizing femtosecond and nanosecond pump−probe spectroscopic methods, the spectral evolution of the CO stretching bands was monitored from 300 fs to tens of microseconds following UV photolysis. The reactive intermediates observed on the ultrafast time scale were also studied using ab initio quantum chemical modeling. It was found that photolysis of the manganese tricarbonyl resulted in dicarbonyls in their singlet or triplet electronic states, whereas photolysis of the rhenium complex led only to the singlet dicarbonyl. The branching ratio of the two manganese intermediates was measured and was related to different electronic excited states. For both the Mn and Re complexes, the reactions were found to be divided into two pathways of distinct time scales by the initial solvation of the dicarbonyls through the Si−H bond or an ethyl group of the solvent molecule. The time scale for the Si−H bond-breaking process was, for the first time, experimentally derived to be 4.4 ps, compared to 230 ns for breaking an alkane C−H bond. Knowledge of the elementary reaction steps including changes in molecular morphology and electronic multiplicity allowed a comprehensive description of the reaction mechanisms for these reactions.

Thermal stability and hydration dynamics of Chymotrypsin Inhibitor 2 in aqueous amino acid solutions from replica exchange molecular dynamics.

Transient anisotropy experiments on the triiodide photodissociation reaction in liquid solution are presented for excitation with 30-fs, 400-nm optical pulses. The decay of the spatial diatomic fragment distribution that is initially created through the process of bond fission occurs on three distinct time scales. On an ultrashort time scale well below 1 ps, an inertial contribution can clearly be distinguished. The corresponding Gaussian decay is described by correlation times around 450 fs. This ultrafast component reflects substantial rotational excitation of the diatomic product which results from impulsive photodissociation of the parent molecule. The contribution of the bending coordinate to the reaction mechanism in liquid solution is emphasized using a simple impulsive model for rotational excitation of the diatomic fragment. An intermediate time scale is characterized by an additional exponential contribution to the anisotropy decay with time constants around 2 ps and coincides with the time scale for vibrational relaxation of the diatomic fragment. On even longer times scales, rotational diffusion of the diatomic fragment governs the anisotropy decay with typical time constants of about 12 ps. A pronounced probe wavelength dependence of the rotational diffusion time constant is explained by an effective hydrodynamic volume that is detected by the probe pulse and originates from the anharmonicity of the diiodide potential. Finally, nuclear coherences at the diiodide vibrational frequency are observed in the inertial decay of the anisotropy. This novel effect is speculated to arise from a coupled motion of the system along all possible bending and stretching coordinates.

At different time scales, a species will experience diverse distribution changes. For Epimedium brevicornum Maxim, the phenomenon is obvious, but the understanding of the spatial dynamics of E. brevicornum under distinct time scales is poor. In this study, we modeled the potential distribution for E. brevicornum for five time scales, 1970–1979, 1980–1989, 1990–1999, 2000–2009, and 2010–2019, with different occurrence data, and the Kuenm package was used to optimize the parameter combination. Then, SDM tools and a Venn diagram were utilized to simulate the changes in highly suitable areas and spatial dynamics, respectively. Comprehensive results show that temperature seasonality (BIO4, 37.54%) has the greatest effect on the distribution of E. brevicornum, followed by minimum temperature (TMIN, 21.42%). The areas of distribution for E. brevicornum are 35.06 × 105 km2, 25.7 × 105 km2, 67.64 × 105 km2, 27.29 × 105 km2, and 9.87× 105 km2, which are mainly concentrated in Gansu, Shaanxi, Shanxi, and Henan, respectively. In addition, the largest regions for expansion, stability, and contraction under various time scales are 5.6 × 105 km2, 3.54 × 105 km2, and 3.47 × 105 km2, respectively. These changes indicate that approximately 7.96% of the regions are highly stable, and three critical counties, Wanyuan, Chenggu, and Hechuan, and Xixiang, have become significant areas for migration. Overall, our results indicate that there are different spatial distribution patterns and dynamics for E. brevicornum for different time scales. Given these results, this study also proposes comprehensive strategies for the conservation and management of E. brevicornum, which will further improve the current resource utilization status.