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This review attempts to situate the emergence of life on the early Earth within the scientific issues of the operational and mechanistic description of life, the conditions and constraints of prebiotic chemistry, together with bottom-up molecular fabrication and biomolecular nanofabrication and top-down miniaturization approaches to the origin of terrestrial life.

We explore charge migration in DNA, advancing two distinct mechanisms of charge separation in a donor (d)-bridge ({Bj})-acceptor (a) system, where {Bj} = B1,B2,⋯ ,BNare the N-specific adjacent bases of B-DNA: (i) two-center unistep superexchange induced charge transfer, d*{Bj}a → d∓{Bj}a±, and (ii) multistep charge transport involves charge injection from d*(or d+) to {Bj}, charge hopping within {Bj}, and charge trapping by a. For offresonance coupling, mechanism i prevails with the charge separation rate and yield exhibiting an exponential dependence$\\propto $exp(-β R) on the d-a distance (R). Resonance coupling results in mechanism ii with the charge separation lifetime$\\tau \\propto $Nηand yield Y ≃ (1 +$\\overline{\\delta}$Nη)-1exhibiting a weak (algebraic) N and distance dependence. The power parameter η is determined by charge hopping random walk. Energetic control of the charge migration mechanism is exerted by the energetics of the ion pair state d∓B1 ±B2⋯ BNa relative to the electronically excited donor doorway state d*B1B2⋯ BNa. The realization of charge separation via superexchange or hopping is determined by the base sequence within the bridge. Our energetic-dynamic relations, in conjunction with the energetic data for d*/d-and for B/B+, determine the realization of the two distinct mechanisms in different hole donor systems, establishing the conditions for ``chemistry at a distance'' after charge transport in DNA. The energetic control of the charge migration mechanisms attained by the sequence specificity of the bridge is universal for large molecular-scale systems, for proteins, and for DNA.

The fundamental mechanisms of charge migration in DNA are pertinent for current developments in molecular electronics and electrochemistry-based chip technology. The energetic control of hole (positive ion) multistep hopping transport in DNA proceeds via the guanine, the nucleobase with the lowest oxidation potential. Chemical yield data for the relative reactivity of the guanine cations and of charge trapping by a triple guanine unit in one of the strands quantify the hopping, trapping, and chemical kinetic parameters. The hole-hopping rate for superexchange-mediated interactions via two intervening AT base pairs is estimated to be 109s-1at 300 K. We infer that the maximal distance for hole hopping in the duplex with the guanine separated by a single AT base pair is 300± 70 angstrom. Although we encounter constraints for hole transport in DNA emerging from the number of the mediating AT base pairs, electron transport is expected to be nearly sequence independent because of the similarity of the reduction potentials of the thymine and of the cytosine.

Ultrafast cluster dynamics encompasses femtosecond nuclear dynamics, attosecond electron dynamics, and electron-nuclear dynamics in ultraintense laser fields (peak intensities$10^{15}-10^{20}$W·cm⁻²). Extreme cluster multielectron ionization produces highly charged cluster ions, e.g.,$(C^{4+}(D^{+})_{4})_{n}$and$(D^{+}I^{22+})_{n}$at$I_{M} = 10^{18}$W·cm⁻², that undergo Coulomb explosion (CE) with the production of high-energy (5 keV to 1 MeV) ions, which can trigger nuclear reactions in an assembly of exploding clusters. The laser intensity and the cluster size dependence of the dynamics and energetics of CE of$(D_{2})_{n}$,$(HT)_{n}$,$(CD_{4})_{n}$,$(DI)_{n}$,$(CD_{3}I)_{n}$, and$(CH_{3}I)_{n}$clusters were explored by electrostatic models and molecular dynamics simulations, quantifying energetic driving effects, and kinematic run-over effects. The optimization of table-top dd nuclear fusion driven by CE of deuterium containing heteroclusters is realized for lightheavy heteroclusters of the largest size, which allows for the prevalence of cluster vertical ionization at the highest intensity of the laser field. We demonstrate a 7-orders-of-magnitude enhancement of the yield of dd nuclear fusion driven by CE of light-heavy heteroclusters as compared with$(D_{2})_{n}$clusters of the same size. Prospective applications for the attainment of table-top nucleosynthesis reactions, e.g.,$^{12}C(P,\\gamma)^{13}N$driven by CE of$(CH_{3}I)_{n}$clusters, were explored.

The effect of a solvation on the thermodynamics and kinetics of polyalanine (Ala12) is explored on the basis of its energy landscapes in vacuum and in an aqueous solution. Both energy landscapes are characterized by two basins, one associated with α-helical structures and the other with coil and β-structures of the peptide. In both environments, the basin that corresponds to the α-helical structure is considerably narrower than the basin corresponding to the β-state, reflecting their different contributions to the entropy of the peptide. In vacuum, the α-helical state of Ala12 constitutes the native state, in agreement with common helical propensity scales, whereas in the aqueous medium, the α-helical state is destabilized, and the β-state becomes the native state. Thus solvation has a dramatic effect on the energy landscape of this peptide, resulting in an inverted stability of the two states. Different folding and unfolding time scales for Ala12 in hydrophilic and hydrophobic chemical environments are caused by the higher entropy of the native state in water relative to vacuum. The concept of a helical propensity has to be extended to incorporate environmental solvent effects.

Nanointerfaces of mobile, thin spherical shells of light ions that expand on the femtosecond time scale, can be produced by Coulomb explosion of extremely ionized molecular heteroclusters consisting of light and heavy ions, e.g., ( D+Iq+)n(q = 7-35), which are generated in ultraintense laser fields (intensity, I,=1016to 1020W· cm-2). Modeling, together with molecular dynamics simulations, reveals the expansion of 2D monolayers with high energies and narrow energy distributions [e.g., Eav≃ 23 keV and Δ E/Eav=0.16 for D+from ( D+I25+)2171] arising from kinematic run-over effects. The expanding regular, monoionic, spherical nanointerfaces manifest the attainment of transient self-organization in complex systems driven by repulsive Coulomb interactions.

Logarithmic oscillations superimposed on the temporal relaxation patterns of complex systems are considered from the standpoint of their hierarchical origin. We propose that a closer examination of experimental data should reveal logarithmic oscillations in systems that are characterized by a hierarchical structure of their dynamical degrees of freedom. On that footing, a new methodology of data analysis is proposed that may prove important for the dynamics of protein folding and of conformational fluctuations in proteins in which the relevant time scales of the dynamical evolution underlying the relaxation kinetics can be deduced from these oscillations.

When DNA-binding proteins search for their specific binding site on a DNA molecule they alternate between linear 1-dimensional diffusion along the DNA molecule, mediated by nonspecific binding, and 3-dimensional volume excursion events between successive dissociation from and rebinding to DNA. If the DNA molecule is kept in a straight configuration, for instance, by optical tweezers, these 3-dimensional excursions may be divided into long volume excursions and short hops along the DNA. These short hops correspond to immediate rebindings after dissociation such that a rebinding event to the DNA occurs at a site that is close to the site of the preceding dissociation. When the DNA molecule is allowed to coil up, immediate rebinding may also lead to so-called intersegmental jumps, i. e., immediate rebindings to a DNA segment that is far away from the unbinding site when measured in the chemical distance along the DNA, but close by in the embedding 3-dimensional space. This effect is made possible by DNA looping. The significance of intersegmental jumps was recently demonstrated in a single DNA optical tweezers setup. Here we present a theoretical approach in which we explicitly take the effect of DNA coiling into account. By including the spatial correlations of the short hops we demonstrate how the facilitated diffusion model can be extended to account for intersegmental jumping at varying DNA densities. It is also shown that our approach provides a quantitative interpretation of the experimentally measured enhancement of the target location by DNA-binding proteins.

We study the survival of a prey that is hunted by N predators. The predators perform independent random walks on a square lattice with V sites and start a direct chase whenever the prey appears within their sighting range. The prey is caught when a predator jumps to the site occupied by the prey. We analyze the efficacy of a lazy, minimal-effort evasion strategy according to which the prey tries to avoid encounters with the predators by making a hop only when any of the predators appears within its sighting range; otherwise the prey stays still. We show that if the sighting range of such a lazy prey is equal to 1 lattice spacing, at least 3 predators are needed in order to catch the prey on a square lattice. In this situation, we establish a simple asymptotic relation lnP ev(t) ~ (N/V)²lnP imm(t) between the survival probabilities of an evasive and an immobile prey. Hence, when the density ρ = N/V of the predators is low, ρ << 1, the lazy evasion strategy leads to the spectacular increase of the survival probability. We also argue that a short-sighting prey (its sighting range is smaller than the sighting range of the predators) undergoes an effective superdiffusive motion, as a result of its encounters with the predators, whereas a far-sighting prey performs a diffusive-type motion.

Ultrafast lasers are versatile tools used in many scientific areas, from welding to eye surgery. They are also used to coherently manipulate light-matter interactions such as chemical reactions, but so far control experiments have concentrated on cleavage or rearrangement of existing molecular bonds. Here we demonstrate the synthesis of several molecular species starting from small reactant molecules in laser-induced catalytic surface reactions, and even the increase of the relative reaction efficiency by feedback-optimized laser pulses. We show that the control mechanism is nontrivial and sensitive to the relative proportion of the reactants. The control experiments open up a pathway towards photocatalysis and are relevant for research in physics, chemistry, and biology where light-induced bond formation is important.