Potential Energy Wells Research Articles

Classical modeling of non-sequential double ionization: Recollision, time-delayed ionization, drift, and possible reattachment

We employ 3d classical ensembles to study Non-Sequential Double Ionization (NSDI) of atoms by strong laser fields at visible and infrared wavelengths. We consider in particular the wavelength dependence of final electron drift directions and the net momentum spectra parallel to the laser polarization. We find that as the wavelength is increased the spectrum transitions from a singlet to a doublet, then to a triplet, and finally back to a doublet. We also show that electrons that escape the central potential-energy well during the pulse may nonetheless be bound to the nucleus after laser turnoff.

Ordering of Poly(3-hexylthiophene) Nanocrystallites on the Basis of Substrate Surface Energy

Molecular dynamics simulations are used to study the influence of functionalized substrates on the orientation of poly(3-hexylthiophene) (P3HT) nanocrystallites, which in turn plays a critical role in P3HT-based transistor performance. The effects of alkyl-trichlorosilane self-assembled monolayer packing density, packing order, and end-group functionality are independently investigated. Across these factors, the potential energy surface presented by the substrate to the P3HT molecules is determined to be the main driver of P3HT ordering. Surprisingly, disordered substrates with a smoothly varying potential energy landscape are found to encourage edge-on P3HT orientation, while highly ordered substrates have undesirable potential energy wells that reduce the edge-on orientation of P3HT because of substrate-side-chain interactions.

Escape from Elliptic Orbit Using Constant Radial Thrust

HE classical problem of escape from a circular orbit using aconstant radial thrust was first proposed by Tsien [1] and thenrefined by Battin [2]. The same problem was then revisited byPrussing and Coversone [3], providing more analytical results andintroducing the concept of a potential-energy well. The aim of thisNote is to show that the available results for circular orbits can beextended to elliptic orbits. In particular, two main issues arepresented: 1) analytical expressions (in terms of propulsiveacceleration)fortheoccurrenceofanescapeconditionand2)simpleformulas for the maximum amplitude of the radial oscillation ifescapedoesnotoccur.Althoughthefollowingdiscussionisgeneral,amissionwithaconstantradialthrustmaybeinterpretedasaspecialcaseofminimagnetosphericplasmapropulsion[4](M2P2)inwhichthe M2P2 system uses a nuclear power source [5].

Ageing under oscillatory stress: Role of energy barrier distribution in thixotropic materials

In this work the ageing dynamics of soft solids of aqueous suspension of laponite has been investigated under the oscillatory stress field. We observed that, at small stresses elastic and viscous moduli showed a steady rise with the elastic modulus increasing at a faster rate than the viscous modulus. However, at higher stresses both the moduli underwent a sudden rise by several orders of magnitude with the onset of rise getting shifted to a higher age for a larger shear stress. We believe that the observed behavior is due to interaction of barrier height distribution of the potential energy wells in which the particle is trapped and strain induced potential energy enhancement of the particles. Strain induced in the material causes yielding of the particles that are trapped in the shallower wells. Those trapped in the deeper wells continue to age enhancing the cage diffusion timescale and consequently the viscosity, which lowers the magnitude of strain allowing more particles to age. This coupled dependence of strain, viscosity and ageing causes forward feedback for a given magnitude of stress leading to sudden rise in both the moduli. Changing the microstructure of the laponite suspension by adding salt affected the barrier heights distribution that showed a profound influence on the ageing behavior. Interestingly, this study suggests a possibility that any apparently yielded material with negligible elastic modulus may get jammed at a very large waiting time.

Light-Induced Excited Spin State Trapping: Ab Initio Study of the Physics at the Molecular Level

This paper provides a qualitative analysis of the physical content of the low-energy states of a spin-transition compound presenting a light-induced excited spin state trapping (LIESST) phenomenon, namely, [Fe(dipyrazolpyridine)2](BF4)2, which has been studied using the wave function-based CASPT2 method. Both the nature of the low-energy states and the relative position of their potential energy wells as a function of the geometry are rationalized from the analysis of the different wave functions. It is shown that the light-induced spin transition occurring in such systems could follow several pathways involving different excited spin states. In an ideal octahedral geometry, the interconversion from the excited singlet state to the triplet of lower energy, which is usually seen as an intermediate state in the LIESST mechanism, is quite unlikely since there is no crossing between the potential energy curves of these two states. On the contrary, in lower-symmetry complexes, the geometrical distortion of the coordination sphere due to ligand constraints is responsible for the occurrence of a crossing between these two states in the Franck-Condon region, leading to a possible participation of this triplet state in the LIESST mechanism. In the reverse LIESST process, a crossing between the potential energy curves of another triplet state and the excited quintet state occurs in the Franck-Condon region as well.

Starch phosphorylation—Maltosidic restrains upon 3′‐ and 6′‐phosphorylation investigated by chemical synthesis, molecular dynamics and NMR spectroscopy

Phosphorylation is the only known in vivo substitution of starch, yet no structural evidence has been provided to explain its implications of the amylosidic backbone and its stimulating effects on starch degradation in plants. In this study, we provide evidence for a major influence on the glucosidic bond in starch specifically induced by the 3-O-phosphate. Two phosphorylated maltose model compounds were synthesized and subjected to combined molecular dynamics (MD) studies and 950 MHz NMR studies. The two phosphorylated disaccharides represent the two possible phosphorylation sites observed in natural starches, namely maltose phosphorylated at the 3'- and 6'-position (maltose-3'-O-phosphate and maltose-6'-O-phosphate). When compared with maltose, both of the maltose-phosphates exhibit a restricted conformational space of the alpha(1-->4) glycosidic linkage. When maltose is phosphorylated in the 3'-position, MD and NMR show that the glucosidic space is seriously restricted to one narrow potential energy well which is strongly offset from the global potential energy well of maltose and almost 50 degrees degrees from the Phi angle of the alpha-maltose crystal structure. The driving force is primarily steric, but the configuration of the structural waters is also significantly altered. Both the favored conformation of the maltose-3'-phosphate and the maltose-6'-phosphate align well into the 6-fold double helical structure of amylopectin when the effects on the glucosidic bond are not taken into account. However, the restrained geometry of the glucosidic linkage of maltose-3'-phosphate cannot be accommodated in the helical structure, suggesting a major local disturbing effect, if present in the starch granule semi-crystalline lattice.

An analysis of the correlation energy contribution to the interaction energy of inert gas dimers

An accurate description of electron correlation is essential for the calculation of interaction energies in cases where dispersion energy is a major component, for example, for the rare gas atoms, physisorption on graphite, and graphene-graphene interactions. Such calculations are computationally demanding using supermolecule methods and the energies calculated lack a simple, physical interpretation. Alternatively density functional theories (DFTs) may be used to give an approximate estimate of the correlation energy. However, the physical nature of this DFT estimate of electron correlation energy is not well understood and, in fact, most current DFT methods do not describe dispersion energy at all. Hence, an analysis of the correlation energy contribution to interaction energies where dispersion energy is important is needed. In order to do this we provide an analysis of the correlation energy contribution to the potential energy curves of He(2), Ne(2), and Ar(2) in terms of the Hartree-Fock (HF) interaction term DeltaE(int) (HF), a dispersion energy term E(disp) and an electron correlation term DeltaE(int) (C). DeltaE(int) (C) includes all other correlation energy effects besides E(disp) and is shown to be repulsive, of a similar short range character to, but of smaller magnitude than DeltaE(int) (HF). This analysis was used to develop a theoretical model which gives a very good estimate of the potential energy wells for He(2), Ne(2), Ar(2), HeNe, HeAr, and NeAr.

Influence of Nonconservative Optical Forces on the Dynamics of Optically Trapped Colloidal Spheres: The Fountain of Probability

We demonstrate both experimentally and theoretically that a colloidal sphere trapped in a static optical tweezer does not come to equilibrium, but rather reaches a steady state in which its probability flux traces out a toroidal vortex. This nonequilibrium behavior can be ascribed to a subtle bias of thermal fluctuations by nonconservative optical forces. The circulating sphere therefore acts as a Brownian motor. We briefly discuss ramifications of this effect for studies in which optical tweezers have been treated as potential energy wells.

A new potential energy surface for OH(A Σ2+)–Ar: The van der Waals complex and scattering dynamics

New ab initio studies of the OH(A (2)Sigma(+))-Ar system reveal significantly deeper potential energy wells than previously believed, particularly for the linear configuration in which Ar is bound to the oxygen atom side of OH(A (2)Sigma(+)). In spite of this difference with previous ab initio work, bound state calculations based on a new RCCSD(T) potential energy surface yield an energy level structure in reasonable accord with previous theoretical and experimental studies. Preliminary open and closed shell quantum mechanical and quasiclassical trajectory scattering calculations are also performed on the new potential energy surface surface. The findings are discussed in the light of previous theoretical and experimental results for rotational energy transfer in collisions of OH(A (2)Sigma(+)) with Ar.

Variational Analysis of the Phenyl + O2 and Phenoxy + O Reactions

Variational transition state analysis was performed on the barrierless phenyl + O2 and phenoxy + O association reactions. In addition, we also calculated rate constants for the related vinyl radical (C2H3) + O2 and vinoxy radical (C2H3O) + O reactions and provided rate constant estimates for analogous reactions in substituted aromatic systems. Potential energy scans along the dissociating C-OO and CO-O bonds (with consideration of C-OO internal rotation) were obtained at the O3LYP/6-31G(d) density functional theory level. The CO-O and C-OO bond scission reactions were observed to be barrierless, in both phenyl and vinyl systems. Potential energy wells were scaled by G3B3 reaction enthalpies to obtain accurate activation enthalpies. Frequency calculations were performed for all reactants and products and at points along the potential energy surfaces, allowing us to evaluate thermochemical properties as a function of temperature according to the principles of statistical mechanics and the rigid rotor harmonic oscillator (RRHO) approximation. The low-frequency vibrational modes corresponding to R-OO internal rotation were omitted from the RRHO analysis and replaced with a hindered internal rotor analysis using O3LYP/6-31G(d) rotor potentials. Rate constants were calculated as a function of temperature (300-2000 K) and position from activation entropies and enthalpies, according to canonical transition state theory; these rate constants were minimized with respect to position to obtain variational rate constants as a function of temperature. For the phenyl + O2 reaction, we identified the transition state to be located at a C-OO bond length of between 2.56 and 2.16 A (300-2000 K), while for the phenoxy + O reaction, the transition state was located at a CO-O bond length of 2.00-1.90 A. Variational rate constants were fit to a three-parameter form of the Arrhenius equation, and for the phenyl + O2 association reaction, we found k(T) = 1.860 x 1013T-0.217 exp(0.358/T) (with k in cm3 mol-1 s-1 and T in K); this rate equation provides good agreement with low-temperature experimental measurements of the phenyl + O2 rate constant. Preliminary results were presented for a correlation between activation energy (or reaction enthalpy) and pre-exponential factor for heterolytic O-O bond scission reactions.

A method of accelerating molecular dynamics simulation for atomic diffusion in metallic interface

Many interesting long-time dynamic properties of solid interface, such as deep diffusion, pervasion and phase forming, cannot be simulated directly using traditional molecular dynamics (MD) because of nanosecond timescale limitations. Thus, a simpler bias potential form has been proposed within the Voter's hyper dynamics scheme. In this method, the potential energy wells are raised by adding a coefficient, which was defined as the accelerating factor, to the original potential. So, the escape rate from potential wells was enhanced, which extends the timescale by several orders of magnitude comparing to the traditional MD simulations. What's more important, the features of potential surface are reserved even without any in_advance knowledge of the location of either the potential energy wells or saddle points. We demonstrate this method by applying it to the mutual diffusion of atoms in Mg/Zn interface with different accelerating factors using a simple Lennard-Jones potential. The results showed that long-time MD simulation can be realized very easily by our approach.

The role of kinetics of and amide bonding in protein stability.

The physical properties and function of biological tissues depend critically upon the hydration of proteins; in particular, their thermal, mechanical, and chemical stability. Here, we show quantitatively how thermal, mechanical, and chemical conditions can denature a protein. An elastic instability criterion is applied to localised ab initio quantum mechanics simulations of water and amide bond energies to predict both denaturing conditions and the effect of water on the glass transition temperature of a protein. The kinetics of bond instability for denaturation over a wide range of time scales is quantified by an expression for a second order phase change using parameters derived directly from the quantum simulations. We also show how the zero point energy of vibrations in a potential energy well of intermolecular bonding can differentiate between crystal and amorphous states of matter and their corresponding transition temperatures; this is illustrated by calculating the crystal melt and glass transition temperatures of water.

The photophysics of 7H-adenine: A quantum chemical investigation including spin–orbit effects

Vertical and adiabatic electronic spectra have been investigated by means of combined density functional and multi-reference configuration interaction methods. Spin–orbit coupling has been determined employing a non-empirical spin–orbit mean-field operator. In the vertical absorption spectrum of isolated 7H-adenine, the transitions to the lowest 1 ( n → π L ∗ ) state, the optically bright 1 ( π H → π L ∗ ) state, and a so far unknown 1(π H → (Ryd, σ ∗)) state are predicted to lie very close to each other. The strong 1 ( π H → π L ∗ ) transition at 4.8 eV is the lowest excitation of 1(π → π ∗) type in 7H-adenine. It is red shifted by about 0.3 eV with respect to the corresponding excitation in the 9H-tautomer. We find the global minimum on the S 1 potential energy hypersurface at about 4.2 eV for a 1 ( n → π L ∗ ) electronic structure. A potential well with a minimum at 4.3 eV exhibits mixed 1 ( n → π L ∗ ) / 1 ( π H → π L ∗ ) character. A planar 1 ( π H → π L ∗ ) structure with a potential energy of 4.6 eV constitutes a stationary point on the S 1 surface. At the present stage it is unclear whether it corresponds to a minimum or a saddle-point. The lowest-lying 1(π → (Ryd, σ ∗)) state is metastable with respect to N 7–H 14 bond dissociation. Its inner (Rydberg) potential well with an adiabatic excitation energy of 4.6 eV represents another minimum on the S 1 PEH. From the theoretical results presented in this work, we conclude that isolated 7H-adenine will be able to emit photons for excitation energies below 4.7 eV(264 nm). Above this threshold singlet excited 7H-adenine can undergo ultrafast non-radiative relaxation to the electronic ground state, either by hydrogen detachment via the 1(π → (Ryd, σ ∗)) channel or via a conical intersection of the 1 ( π H → π L ∗ ) state along a ring puckering mode. The 3 ( π H → π L ∗ ) T 1 state can be efficiently populated via intersystem crossing from one of the S 1 potential energy wells. Large-amplitude motions in the T 1 state along an out-of-plane distortional coordinate lead to significant configuration interaction of the 1 ( n → π L ∗ ) and 1 ( π H → π L ∗ ) structures which lend intensity to the phosphorescence.

Human Identification From Dental X-Ray Images Based on the Shape and Appearance of the Teeth

Dental biometrics deal with human identification from dental characteristics. In this paper, we present a new technique for identifying people based upon shapes and appearances of their teeth from dental X-ray radiographs. The new technique represents each tooth by a feature vector obtained from the forcefield energy function of the grayscale image of the tooth and Fourier descriptors of the contour of the tooth. The feature vector is composed of the distances between a small number of potential energy wells as well as a small number of Fourier descriptors. Given a query image (i.e., postmortem radiograph), each tooth is matched with the archived teeth in the database (antemortem radiographs) that have the same tooth number. Then, voting is used to obtain a list of best matches for the query image based upon the matching results of the individual teeth. Our goal of using appearance and shape-based features together is to overcome the drawback of using only the contour of the tooth, which can be strongly affected by the quality of the images. The experimental results on a database of 162 antemortem images show that our method is effective in identifying individuals based on their dental radiographs

Microfluidic self-assembly of live Drosophila embryos for versatile high-throughput analysis of embryonic morphogenesis

A method for assembling Drosophila embryos in a microfluidic device was developed for studies of thermal perturbation of early embryonic development. Environmental perturbation is a complimentary method to injection of membrane-impermeable macromolecules for assaying genetic function and investigating robustness in complex biochemical networks. The development of a high throughput method for perturbing embryos would facilitate the isolation and mapping of signaling pathways. We immobilize Drosophila embryos inside a microfluidic device on minimal potential-energy wells created through surface modification, and thermally perturb these embryos using binary laminar flows of warm and cold solutions. We self-assemble embryos onto oil adhesive pads with an alcohol surfactant carrier fluid (detachment: 0.1 mL/min), and when the surfactant is removed, the embryo-oil adhesion increases to approximately 25 mL/min flow rates, which allows for high velocities required for sharp gradients of thermal binary flows. The microfluidic thermal profile was numerically characterized by simulation and experimentally characterized by fluorescence thermometry. The effects of thermal perturbation were observed to induce abnormal morphogenetic movements in live embryos by using time-lapse differential interference contrast (DIC) microscopy.

Catastrophe Observation in a Josephson-Junction System

We report on experiments performed to probe quantum coherence in a system consisting of an rf-SQUID in which the Josephson junction is replaced by a small loop containing two junctions in parallel. At temperatures of the order of 10 mK the system may develop three potential energy wells, which modify the usual two well energy profile and thereby verify the qubit manipulation strategy. The appearance of the third potential well can be interpreted as evidence of a butterfly catastrophe, namely, a catastrophe expected for a system described by four control parameters and one state variable.

Experimental and Master Equation Study of the Kinetics of OH + C2H2: Temperature Dependence of the Limiting High Pressure and Pressure Dependent Rate Coefficients

The kinetics of the reaction OH + C2H2 have been studied using laser flash photolysis at 248 nm to generate OH radicals and laser-induced fluorescence to monitor OH removal. An attempt was made to use the rate coefficients OH (v = 1,2) + C2H2 to determine the limiting high-pressure rate coefficient, k(1a)(infinity), over the temperature range of 195-823 K. This method is usually applicable if the reaction samples the potential energy well of the adduct, HOC2H2, and if intramolecular vibrational relaxation is fast. In the present case, however, the rate coefficients for loss of the vibrationally excited states by reaction with C2H2 also contain a substantial contribution from nonreactive vibrational relaxation, which occurs via a mechanism that does not sample the adduct potential energy well but involves, at least at low temperatures, collisions that access a shallower, longer range van der Waals well. The data were analyzed using a composite mechanism that incorporates both reactive and nonreactive energy transfer mechanisms, which allows the determination of k(1a)(infinity)(T) for OH + C2H2 with satisfactory accuracy over the temperature range 195-823 K. The kinetics of the reaction OH (v = 0) + C2H2 were also studied in He over the range of conditions: 210-373 K and 5-760 Torr. A one-dimensional master equation (ME) analysis of the experimental data provided a further determination of k(1a)(infinity)(T) and also <DeltaE>(down) for He. Combining the two sets of results gives a consistent dataset for k(1a)(infinity) and the Arrhenius parameters A1ainfinity = 7.3 x 10(-12) cm(3) molecule(-1) s(-1) and E(1a)(infinity) = 5.3 kJ mol(-1), with <DeltaE>(down) = 150(T/300 K) cm(-1). Additional experiments were conducted at room temperature in N(2) and SF(6) by laser flash photolysis with cavity ring down spectroscopy, and ME calculations were then optimized for the pressure falloff in N(2) by varying the average downward energy transfer parameter (<DeltaE>(down)). The output from the best fit ME was parametrized using a modified Troe expression to provide rate data for use in atmospheric modeling.

The influence of hydrogen bonds on electron transfer rate in photosynthetic RCs

Hydrogen bonds formed between photosynthetic reaction centers (RCs) and their cofactors were shown to affect the efficacy of electron transfer. The mechanism of such influence is determined by sensitivity of hydrogen bonds to electron density rearrangements, which alter hydrogen bonds potential energy surface. Quantum chemistry calculations were carried out on a system consisting of a primary quinone Q A, non-heme Fe 2+ ion and neighboring residues . The primary quinone forms two hydrogen bonds with its environment, one of which was shown to be highly sensitive to the Q A state. In the case of the reduced primary quinone two stable hydrogen bond proton positions were shown to exist on [Q A-His M219] hydrogen bond line, while there is only one stable proton position in the case of the oxidized primary quinone. Taking into account this fact and also the ability of proton to transfer between potential energy wells along a hydrogen bond, theoretical study of temperature dependence of hydrogen bond polarization was carried out. Current theory was successfully applied to interpret dark P +/Q A − recombination rate temperature dependence.

Electrostatically telescoping nanotube nonvolatile memory device

We propose a nonvolatile memory based on carbon nanotubes (CNTs) serving as the keybuilding blocks for molecular-scale computers and investigate the dynamic operations of adouble-walled CNT memory element by classical molecular dynamics simulations. Thelocalized potential energy wells achieved from both the interwall van der Waals energy andCNT–metal binding energy make the bistability of the CNT positions and the electrostaticattractive forces induced by the voltage differences lead to the reversibility of this CNTmemory. The material for the electrodes should be carefully chosen to achieve thenonvolatility of this memory. The kinetic energy of the CNT shuttle experiences severalrebounds induced by the collisions of the CNT onto the metal electrodes, and this iscritically important to the performance of such an electrostatically telescoping CNTmemory because the collision time is sufficiently long to cause a delay of the statetransition.

Colloidal transport through optical tweezer arrays

Viscously damped particles driven past an evenly spaced array of potential energy wells or barriers may become kinetically locked in to the array, or else may escape from the array. The transition between locked-in and free-running states has been predicted to depend sensitively on the ratio between the particles' size and the separation between wells. This prediction is confirmed by measurements on monodisperse colloidal spheres driven through arrays of holographic optical traps.