Exact scattering length for a potential of Lennard-Jones type

For a modified Lennard-Jones interaction potential of the form ∼[(r₀/r)^2n-2-(r₀/r)ⁿ], an exact and simple expression for the s-wave scattering length is presented, and discussed in some detail. For heavy alkali atoms, which nowadays are routinely being employed to produce Bose-Einstein condensates, this potential is well compatible with known experimental data when n = 6.     

Effects of NH3, O2, and N2 co-implantation on Cu out-diffusion and antimicrobial properties of copper plasma-implanted polyethylene

Metal antibacterial reagents are effective in the enhancement of the antimicrobial properties of medical polymers. However, incorporation of metal antibacterial reagents into polymers using conventional methods usually results in unstable antimicrobial effects. Our previous research demonstrates that plasma immersion ion implantation (PIII) can be used to effectively incorporate metal antibacterial reagents such as Cu into polyethylene (PE) in the near surface region up to several hundred nanometers without causing noticeable damage to the polymer matrix. In this work, various gases including NH₃, O₂, and N₂ were plasma-implanted in concert with Cu plasma immersion ion implantation to study the effects of these gas species on the release rate of Cu from the substrate. Our experimental results reveal that the copper depth profiles are not affected significantly by NH₃, O₂, or N₂ co-implantation and these gas elements have similar depth profiles as Cu. Chemical analyses demonstrate that polar functional CO, CO, CN, CN, and CN bonds formed in the substrate play an important role in regulating Cu out-diffusion. Among the three gas species, N₂ shows the best effects in regulating Cu out-diffusion and produces the best long term antibacterial properties. The Cu retention and out-diffusion mechanism in the ion-implanted polyethylene is described.     

Accurate calculation of the scattering length for the cooling of hydrogen atoms by lithium atoms

An improved ab initio calculation has been performed for the potential for the LiH a ³Σ⁺ state, using two very large basis sets. The Basis Set Superposition Error (BSSE) correction has been determined for both basis sets and the non-Born-Oppenheimer correction estimated to be negligible. The best potential is approximately 10% deeper than the previous estimate. Vibrational energies and scattering lengths have been calculated for ^6,7LiH(D) with both potentials, with and without the BSSE correction, and also with an estimated potential expected to bracket the true potential. The ⁷LiH scattering length is estimated to be (45 ± 4)a₀ and hence the low-energy cross-section in the best a ³Σ⁺ potential is about half that calculated previously. Enhanced cooling by ⁷Li of trapped H atoms remains feasible. Received 30 April 2001     

Activated dynamics of semiflexible polymers on structured substrates

We study the thermally activated motion of semiflexible polymers in double-well potentials using field-theoretic methods. Shape, energy, and effective diffusion constant of kink excitations are calculated, and their dependence on the bending rigidity of the semiflexible polymer is determined. For symmetric potentials, the kink motion is purely diffusive whereas kink motion becomes directed in the presence of a driving force. We determine the average velocity of the semiflexible polymer based on the kink dynamics. The Kramers escape over the potential barriers proceeds by nucleation and diffusive motion of kink-antikink pairs, the relaxation to the straight configuration by annihilation of kink-antikink pairs. We consider both uniform and point-like driving forces. For the case of point-like forces the polymer crosses the potential barrier only if the force exceeds a critical value. Our results apply to the activated motion of biopolymers such as DNA and actin filaments or of synthetic polyelectrolytes on structured substrates.     

Growth of attached actin filaments

In several studies of actin-based cellular motility, the barbed ends of actin filaments have been observed to be attached to moving obstacles. Filament growth in the presence of such filament-obstacle interactions is studied via Brownian dynamics simulations of a three-dimensional energy-based model. We find that with a binding energy greater than 24k _B T and a highly directional force field, a single actin filament is able to push a small obstacle for over a second at a speed of half of the free filament elongation rate. These results are consistent with experimental observations of plastic beads in cell extracts. Calculations of an external force acting on a single-filament-pushed obstacle show that for typical in vitro free-actin concentrations, a 3pN pulling force maximizes the obstacle speed, while a 4pN pushing force almost stops the obstacle. Extension of the model to treat beads propelled by many filaments suggests that most of the propulsive force could be generated by attached filaments.     

Localization properties of electronic states in a polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.     

Quantum diffusion in polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate quantum diffusion of an electron in a model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with fluctuation of the parameters due to the impact of colored noise. The randomness is introduced by fluctuations of distance between two consecutive bases along the stacked base pairs. We demonstrate that in the model the decay time of the correlation can control the spread of the electronic wavepacket. Furthermore it is shown that in a motional narrowing regime the averaging over fluctuation causes ballistic propagation of the wavepacket, and in the adiabatic regime the electronic states are affected by localization.     

Counterion vibrations in the DNA low-frequency spectra

The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na⁺ , K⁺ , Rb⁺ and Cs⁺ the frequency of ion-phosphate vibrations decreases from 174 to 96cm^-1 as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na⁺ do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs⁺ have effect on the internal vibrations of the DNA structural elements.     

Kinetics of protein-release by an aptamer-based DNA nanodevice

A recently introduced DNA nanodevice can be used to selectively bind or release the protein thrombin triggered by DNA effector strands. The release process is not well described by simple first or second order reaction kinetics. Here, fluorescence resonance energy transfer and fluorescence correlation spectroscopy experiments are used to explore the kinetics of the release process in detail. To this end the influence of concentration variations and also of temperature is determined. The relevant kinetic parameters are extracted from these experiments and the kinetic behavior of the system is simulated numerically using a set of rate equations. The hydrodynamic radii of the aptamer device alone and bound to thrombin are determined as well as the dissociation constant for the aptamer device-thrombin complex. The results from the experiments and a numerical simulation support the view that the DNA effector strand first binds to the aptamer device followed by the displacement of the protein.     

Force spectroscopy of single multidomain biopolymers: A master equation approach

Experiments using atomic force microscopy for unfolding single multidomain biopolymers cover a broad range of time scales from equilibrium to non-equilibrium. A master equation approach allows to identify and treat coherently three dynamical regimes for increasing linear ramp velocity: i) an equilibrium regime, ii) a transient regime where refolding events still occur, and iii) a saw-tooth regime without any refolding events. For each regime, analytical approximations are derived and compared to numerically investigated examples. We analyze in the framework of this model also a periodic experimental protocol instead of a linear ramp. In this case, a major simplification arises if the dynamics can be restricted to an effectively two-dimensional subspace. For transitions with an intermediate meta-stable state, like Immunoglobulin27, a refined model allows to extract previously unknown molecular parameters related to this meta-stable state.