Recent advances in quantitative single-cell analysis revealed large diversity gene expression levels between individual cells, which could affect the physiology and/or fate of each cell. In contrast, for most metabolites, concentrations were only measureable as ensemble averages many cells. living adenosine triphosphate (ATP) is a critically important metabolite that powers intracellular reactions. Quantitative measurement absolute ATP concentration cells has not been achieved because lack...

We calculate harmonic spectra and shapes of attosecond-pulse trains using numerical solutions Non-Born-Oppenheimer time-dependent Shr\"odinger equation for 1D ${\mathrm{H}}_{2}$ molecules in an intense laser pulse. A very strong signature nuclear motion is seen the time profiles high-order harmonics. In general shortens part train originating from first electron contribution, but it may enhance second contribution longer pulses. The shape harmonics can thus be used monitoring motion.

Recent developments in transition state theory brought about by dynamical systems are extended to time-dependent such as laser-driven reactions. Using normal form theory, the authors construct a reaction coordinate with regular dynamics inside region. The conservation of associated action enables one extract invariant manifolds that act separatrices between reactive and nonreactive trajectories thus make it possible predict ultimate fate trajectory. They illustrate power our approach on...

Abstract Despite being a promising soft material embodied by molecular self-assembly, the formation mechanism of supramolecular gels remains challenging to fully understand. Here we provide nanoscopic insights into gel-forming fibers from urea derivative. High-speed atomic force microscopy derivative revealed presence lag phase prior fibers, suggesting nucleation process. The fiber growth kinetics differ at both termini fiber, indicating directional hydrogen-bonding motif units, which is...

The generalized Langevin equation (GLE) is extended to the case of nonstationary bath. derivation starts with Hamiltonian motion total system including bath, without any assumption on form or distribution initial condition. Then projection operator formulation utilized obtain a low-dimensional description dynamics surrounded by bath modes. In contrast ordinary GLE, mean force becomes time-dependent function position and velocity system. friction kernel found depend both past current times,...

Nonlinear dynamics around a rank-one saddle is investigated in high energy regime above the reaction threshold. The transition state (TS) considered as surface of "point no return" through which all reactive trajectories pass only once process climbing over before being captured product state. A no-return TS ceases to exist certain regime. However, even at energies where can longer exist, it shown that "an impenetrable barrier" phase space robustly persists, acts boundary between and...

We present a novel theory which enables us to explore the mechanism of reaction selectivity and robust functions in complex systems persisting under thermal fluctuation. The constructs nonlinear coordinate transformation so that equation motion for new is independent other nonreactive coordinates presence In this article we suppose reacting subject noise are described by multidimensional Langevin without priori assumption form potential. composed not only all velocities associated with...

Dynamics of passage over a saddle is investigated for quantum system under the effect time-dependent external field (laser pulse). We utilize recently developed theories nonlinear dynamics in region, and extend them to incorporate both time-dependence mechanical effects system. Anharmonic couplings laser fields with any functional form time dependence are explicitly taken into account. As theory based on Weyl expression mechanics, interpretation facilitated by classical phase space picture,...

A model for large deformation of polymer gels with physical cross-linking is developed and shown to be in good agreement experimental stress-strain curves which show strain hardening intermediate strains followed by softening deformations near the yield strain. The takes into account coil-helix transition equilibrium allows distribution end-to-end distance. gel considered formed long flexible chains crystalline zones acting as junctions chains. number segments contained a chain variable due...

Reactivity boundaries that divide the origin and destination of trajectories are crucial importance to reveal mechanism reactions, which was recently found exist robustly even at high energies for index-one saddles [Phys. Rev. Lett. 105, 048304 (2010)]. Here we revisit concept reactivity boundary propose a more general definition can involve single reaction associated with bottleneck made up higher index and/or several saddle points different indices, where normal form theory, based on...

A new method of fabricating amorphous Si thin film transistors (a-Si TFT's) has been developed. This uses the self-alignment process, which also includes successive deposition gate insulator and active layers in one-pumpdown time an RF glow discharge apparatus. greatly simplifies fabrication process results stable device performance. The practicability this was confirmed by experimentally fabricated devices.

The framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in thermal fluctuation is examined with model system. Numerical simulations are carried out an underdamped Langevin equation Müller–Brown potential surface, which contains three wells and two saddles, compared prediction by theory. Reaction probabilities specific initial conditions system as well their average over Boltzmann distribution investigated position space spanned...

A framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in multidimensional Langevin equation is extended generalized equations without priori assumption forms potential (in general, nonlinearly coupled systems) and friction kernel. The motion with memory effect can be transformed into an at cost increase dimensionality system, hence theoretical (nonlinear) formulation non-Markovian process colored noise. It found that increased...

Nonlinear dynamics in the passage over a rank-one saddle is investigated as function of temperature presence stochastic, thermal fluctuation. The analyses are based on framework we developed recently adopting multidimensional underdamped Langevin equation (without any assumption for form potential mean force). can principle provide single coordinate to enable us predict final destination reaction thermally fluctuating media. At each temperature, preciseness or error evaluated capturing true...

One of the most fundamental problems in studying general Hamiltonian systems with many degrees freedom is to extract a low-dimensional subsystem including essential dynamics. In this paper, new partial normal form (PNF) method developed reduce number coupling terms and simplify dynamics analyses. The PNF allows one decouple unimportant bath modes as well reactive mode from system by assessing significance terms. applied chemical reaction...

A framework to calculate the rate constants of condensed phase chemical reactions manybody systems is presented without relying on concept transition state. The theory based a we developed recently adopting multidimensional underdamped Langevin equation in region rank-one saddle. provides reaction coordinate expressed as an analytical nonlinear functional position coordinates and velocities system (solute), friction constants, random force environment (solvent). Up moderately high...

Many chemical reactions, including those of biological importance, take place in thermally fluctuating environments. Compared to isolated systems, there arise markedly different features due the effects energy dissipation through friction and stochastic driving by random forces reflecting fluctuation environment. Investigation how robustly system reacts under influence thermal fluctuation, elucidating role reaction are significant subjects study reactions. In this article, we start with...

Reactivity boundaries that divide the destination and origin of trajectories are crucial importance to reveal mechanism reactions. We investigate whether such reactivity can be extracted for higher index saddles in terms a nonlinear canonical transformation successful index-one by using model system with an index-two saddle. It is found true do not coincide those taking into account nonlinearity region saddle even small perturbations, discrepancy more pronounced less repulsive direction...

The transition state is fundamental to modern theories of reaction dynamics. While theory (TST) has been used mainly in chemical physics, it can be applied any problem that involves some form transformation, including half-scattering events such as ionization Rydberg atoms. In this paper, we construct the states H+2 an external electric field. process, encounter and eliminate small divisors our perturbation expansion monitor its convergence using a new error criterion. procedure readily...

Gellan gel, a typical polysaccharide is ruptured with different deformation behaviors from gelatin gel or rubber. It exhibits both strain hardening and softening; observed for moderate softening occurs larger strain. From the analyses of stress–strain curves gellan gels, we propose forms energy function. The fit proposed equation was excellent, while existing models fail because they consider only one effect. Furthermore, these equations are shown to be capable extracting effects separately...

The generalized Langevin equation (GLE) is used widely in molecular science and time series analysis as it offers a convenient low-dimensional description for large systems. There the dynamical effect of environment interacting with system expressed friction random force. present paper aims to investigate explicit variables describe modes that are derived from GLE defined solely terms observed variable. formulation results equations motion without memory term hence more intuitive than GLE....

We investigate the harmonic phase dependence of photoionization aligned $\mathrm{H}_{2}{}^{+}$ with three colors: two high-order (uv) harmonics orders $(q+1)$ and $(q\ensuremath{-}1)$ in presence a ``dressing'' ir photon such that absorption one is resonant emission photon. The transition amplitudes for these interfering paths are calculated wide range uv energies, internuclear distances $R$, orientations. relative ionizing photons controls interference between total amplitude, thus allowing...