Protein conformational fluctuations and free-energy transduction

Non-equilibrium fluctuations, whether imposed externally or driven by an energy-releasing chemical reaction, can cause a protein to cycle through several conformations. This cycling can drive a process thermodynamically uphill even though any one conformation considered independently catalyzes the process in the downhill direction. This is because the different conformations have different rate constants (energy barriers) between the states in the catalytic cycle. Even though each conformation individually obeys detailed balance, the flashing between different energy profiles gives rise to a ratchet effect. Further, by exploiting protein conformational dynamics, a single stochastic input can be converted into two phase-shifted internal parameters (e.g. a kinetic barrier height and a binding well energy). This allows the output process to be driven nearly adiabatically, explaining in part the very high efficiencies observed for some biological energy-transduction processes. The results apply equally to driving a biochemical reaction away from equilibrium by an enzyme, to formation of an osmotic gradient across a membrane by a molecular pump, or to motion and generation of force by a molecular motor. Received: 8 February 2002 / Accepted: 4 March 2002 / Published online: 22 April 2002     

Infinitely many shape invariant discrete quantum mechanical systems and new exceptional orthogonal polynomials related to the Wilson and Askey–Wilson polynomials

Two sets of infinitely many exceptional orthogonal polynomials related to the Wilson and Askey–Wilson polynomials are presented. They are derived as the eigenfunctions of shape invariant and thus exactly solvable quantum mechanical Hamiltonians, which are deformations of those for the Wilson and Askey–Wilson polynomials in terms of a degree ?   (?=1,2,…$?=1,2,\dots$) eigenpolynomial. These polynomials are exceptional in the sense that they start from degree ??1$??1$ and thus not constrained by any generalisation of Bochner's theorem.     

Electronic properties close to Dirac cone in two-dimensional organic conductor α-(BEDT-TTF)<Subscript>2</Subscript>I<Subscript>3</Subscript>

A zero-gap state (ZGS) has been found in a bulk system of two-dimensional organic conductor, α-(BEDT-TTF)₂I₃ salt which consists of four sites of donor molecules in a unit cell. In the present paper, the characteristic of the ZGS is analyzed in detail and the electronic properties are examined in the vicinity of the Dirac point where the conduction and valence bands degenerate to form the zero-gap. The eigenvectors of the energy band have four components of respective sites, where two of them correspond to inequivalent sites and the other two correspond to equivalent sites. It is shown that the former exhibits an exotic momentum dependence around the contact point and the latter shows almost a constant dependence. The density of states of each site close to the Dirac point is calculated to demonstrate the temperature dependence of the local magnetic susceptibility and the local nuclear magnetic relaxation rate. Further, the robust property of the ZGS against the anion potential is also shown by using the second-order perturbation.     

Ionic recoil energies in the Coulomb explosion of metal clusters

The photoionization of metal clusters in intense femtosecond laser fields has been studied. In contrast to an experiment on atoms, the interaction in this case leads to a very efficient and high charging of the particle where tens of electrons per atom are ejected from the cluster. The recoil energy distribution of the atomic fragment ions was measured which in the case of lead clusters exceeds 180 keV. Enhanced charging efficiency which we observed earlier for specific pulse conditions is not reflected in the recoil energy spectra. Both the average and the maximum energies decrease with increasing laser pulse width. This is in good agreement with molecular dynamics calculations. Received 20 December 2000     

Strong water repellency effect on SiO<Subscript>2</Subscript> films processed at a nanometric scale

The present study deals with the creation of nano-rough surfaces with stable and controlled high hydrophobicity. These surfaces were obtained by combining the ion track etching technique with a simple functionalization by grafting perfluoroctyltrichlorosilane (PFOTS) molecules. Surface morphology was investigated by AFM observations which evidenced a self-affine fractal structure with a fractal dimension D_f ~ 2.6. The study of the wetting properties of these surfaces allowed to elucidate the conditions for observing a high hydrophobicity phenomenon and to predict the contact angle values for surfaces designed at a nanometric scale.     

Effects of polydispersity on the order-disorder transition of diblock copolymer melts

The effect of polydispersity on an AB diblock copolymer melt is investigated using lattice-based Monte Carlo simulations. We consider melts of symmetric composition, where the B blocks are monodisperse and the A blocks are polydisperse with a Schultz-Zimm distribution. In agreement with experiment and self-consistent field theory (SCFT), we find that polydispersity causes a significant increase in domain size. It also induces a transition from flat to curved interfaces, with the polydisperse blocks residing on the inside of the interfacial curvature. Most importantly, the simulations show a relatively small shift in the order-disorder transition (ODT) in agreement with experiment, whereas SCFT incorrectly predicts a sizable shift towards higher temperatures.     

Phonon effects in tunnelling through a double quantum dot molecule

Phonon effects in tunnelling through a double quantum dot molecule are investigated by use of a recently developed technique, which is based on an exact mapping of a many-body electron-phonon interaction problem onto a multichannel one-body problem. The molecule is sandwiched between two ideal electrodes and the electron at each dot of the molecule interacts independently with Einstein phonons. Single-electron transmission rates through the molecule are computed and the nonlinear spectrum obtained shows a structure with many more satellite peaks due to the excitations of phonons. The strength of resonant peaks is found to be strongly dependent on the number of excited phonons. The effects of electron-phonon interaction on the current and shot noise, depending on the voltage bias applied at the two electrodes as well as the potential energy of the molecule, are discussed.     

High-power laser interactions with nanostructured materials

We use short-pulse high-power lasers to selectively modify the structure of nanolaminates and nanocrystals. It is demonstrated that femtosecond pulses can achieve excellent results for microscopic thin film removal. Laser pulses can also be used to modify the crystal structure of thin films. It is also demonstrated that coherent laser excitation promotes a selective modification of nanocrystals, resulting in changes of size, shape, and crystal structure. Received: 7 October 2002 / Accepted: 20 January 2003 / Published online: 28 May 2003 RID="*" ID="*"Corresponding author. Fax: +1-414/229-5589, E-mail: yakovlev@uwm.edu     

Non-linear scission/recombination kinetics of living polymerization

Living polymers are formed by reversible association of primary units (unimers). Generally the chain statistical weight involves a factor σ < 1 suppressing short chains in comparison with free unimers. Living polymerization is a sharp thermodynamic transition for σ ≪ 1 which is typically the case. We show that this sharpness has an important effect on the kinetics of living polymerization (one-dimensional association). The kinetic model involves i) the unimer activation step (a transition to an assembly-competent state); ii) the scission/recombination processes providing growth of polymer chains and relaxation of their length distribution. Analyzing the polymerization with no chains but unimers at t = 0 , with initial concentration of unimers M ≳ M ^* (M^* is the critical polymerization concentration), we determine the time evolution of the chain length distribution and find that: 1) for M ^* ≪ M ≪ M ^*/σ the kinetics is characterized by 5 distinct time stages demarcated by 4 characteristic times t₁, t₂, t₃ and t^*; 2) there are transient regimes (t ₁ ≲ t ≲ t ₃) when the molecular-weight distribution is strongly non-exponential; 3) the chain scissions are negligible at times shorter than t₂. The chain growth is auto-accelerated for t ₁ ≲ t ≲ t ₂ : the cut-off chain length (= polymerization degree 〈n〉_w N ₁ ∝ t ² in this regime. 4) For t ₂ < t < t ₃ the length distribution is characterized by essentially 2 non-linear modes; the shorter cut-off length N₁ is decreasing with time in this regime, while the length scale N₂ of the second mode is increasing. (5) The terminal relaxation time of the polymer length distribution, t^*, shows a sharp maximum in the vicinity of M^*; the effective exponent is as high as ∼ σ^-1/3 just above M^*.     

Multiple-beam Ramsey interference and quantum decoherence

We study the effect of photon scattering from a path of a four-beam atomic interference setup, which is based on a cesium atomic beam and two subsequent optical Ramsey pulses projecting the atoms onto a multilevel dark state. While in two-beam interference, any attempt to keep track of an interfering path reduces the fringe contrast, we demonstrate that photon scattering in a multiple-path arrangement cannot only lead to a decrease, but - under certain conditions - also to an increase of the interference contrast. The results are confirmed by a density-matrix calculation. We are aware that in all cases the “which-path” information carried away by the scattered photons leads to a loss of information that is contained in the atomic quantum state. An approach to quantify this “which-path” information using observed fringe signals is presented; it allows for an appropriate measure of quantum decoherence in multiple-path interference. Received: 27 July 2000 / Published online: 6 December 2000