Solitary excitations in the α-helix: Viscous and thermal effects

We report a molecular dynamics study of the propagation of a solitary excitation in a one-dimensional Lennard-Jones lattice when thermal and frictional effects are included. We give to the parameters that characterize the system the values of a typical chain of hydrogen-bonded peptide groups in the α-helix and observe that at temperatures and energies of biological interest and with water as a solvent, potential energies can be transported over long distances.     

Theoretical study of the optical and charge transport properties in non-peripherally octasubstituted phthalocyanine–tetrabenzoporphyrin hybrids

The charge transfer rate of seven non-peripherally phthalocyanine–tetrabenzoporphyrin hybrids was investigated theoretically at the level of B3LYP/6-31+G(d,p) using density functional theory. The results showed that the hybrids are semiconductor molecules, which have a certain absorption in the visible region. The hole or electron transport capability of a non-peripherally substituted octamethyl phthalocyanine molecule is obviously better than that of phthalocyanine or non-peripherally substituted octafluorine, octamethoxy phthalocyanine molecules at 300 K, whereas the holes or electron transport capabilities of four non-peripherally substituted octamethoxy phthalocyanine–tetrabenzoporphyrin hybrids are basically the same. Overall, the hole transport capability of hybrids is superior to their electron transport capability. The charge transfer rate constant and the carrier mobility rate of three representative molecules using three methods, that is the long range-corrected functionals CHB-B3LYP and WB97XD, the metahybrid GGA M06-2X functional, are consistent with the use of the density functional B3LYP method.     

Dynamic characterization of charge transport in organic and polymer transistors

In this paper we describe three methods that can be used to measure the transient response of organic and polymer field-effect transistors (FETs) and also how such measurements can be used to determine the drift mobility and velocity. The first method measures the response of a FET to a step voltage applied to the source with the gate grounded and the drain held at close to ground, while the second uses a ramp input to the source. The third technique evaluates the frequency response of the FET, connected as a diode, to a large-signal alternating voltage. We show that important information can be obtained from such measurements which can be quantitatively interpreted with the help of models that we are developing. In general, there is good agreement between the drift mobility measured with these approaches and the field-effect mobility calculated from transistor output and transfer characteristics. The specific results we present in this paper are for pentacene devices; however, other recent work by our group indicates that these results are more general.     

Mutual influence of hydrogen and vacancies in α-zirconium on the energy of their interaction with metal

We presents a first-principles investigation on the interaction energy of hydrogen and vacancies with α-zirconium. It is established that the presence of vacancies in zirconium increases the hydrogen–metal binding energy; the presence of hydrogen in the zirconium lattice reduces the vacancy formation energy. It is shown that hydrogen and vacancies in zirconium form complexes that considerably distort the metal lattice. The increase in the covalency degree of the metal–metal and hydrogen–metal bounds is observed in the vicinity of these complexes.     

On the role of theΔ -isobar in deep inelastic scattering on the deuteron

The role of the nuclear structure effects, viz. the boundness of nucleons and-isobar components, in the deep inelastic scattering of leptons on the deuteron is considered. It is shown that small admixture of the-isobar configurations to the deuteron wave function may lead to significant effects in the spin structure functions of the deuteronb ₁ ^D andg ₁ ^D (x): up to 4% in g ₁ ^D (x) dx and up to 10% ing ₁ ^D (x) at smallx.One of the authors (A.U.) thanks Prof. F.C. Khanna for helpful discussions and for kind offering the information used in our calculations.     

On the response and dissipated energy of Bouc–Wen hysteretic model

An efficient formulation for the response and dissipated energy of Bouc–Wen hysteretic model is proposed. The displacement is associated with the hysteretic parameter in terms of Gauss’ hypergeometric function. The hysteretic equation is solved analytically for specific values of the exponential parameter that controls the transition between elastic and inelastic regime. This formulation is used to provide analytical expressions of the dissipated energy under symmetric cyclic excitation, based solely on the model parameters and the displacement amplitude. For arbitrary values of the exponential parameter, the equations are solved numerically. For fully yielding systems, approximate relations are determined using suitable curve fitting. The derived expressions facilitate considerably the preliminary design of hysteretic systems.     

On the issue of zero point energy in Bose–Einstein condensates

Following on our earlier work in this area, here we examine in some detail the physical mechanism involved in the Bose–Einstein condensation process. In particular we emphasise the significance of the zero value of the chemical potential at and below the critical temperature. The molar zero-point energy (ZPE) for an ideal gas of He⁴ atoms in our new analysis is estimated and found to be very close to that calculated for an ideal Fermi gas of He³ atoms under the same conditions. This gives numerical support to our theory. We also show how the theory is consistent with the presence of a density maximum in liquid He⁴.     

Nature of charge carriers in disordered molecular solids: are polarons compatible with observations?

Polaronic theories for charge transport in disordered organic solids, particularly molecularly doped polymers, have been plagued by issues of internal consistency related to the magnitude of physical parameters. We present a natural resolution of the problem by showing that, in the presence of correlated disorder, polaronic carriers with binding energies Delta approximately 50-500 meV and transfer integrals J approximately 1-20 meV are completely consistent with the magnitudes of field and temperature dependent mobilities observed.     

On the role of Δ-resonance in the pion production in collisions of heavy intermediate-energy ions in the hydrodynamic approach

Pion production in heavy-ion collisions is considered within the hydrodynamic approach. It is shown that consideration of pion production as a result of Δ-resonance decay (Δ → N + π) leads to hardening of the high-energy “tails” of subthreshold pions.     

Exact thermodynamics of pairing and charge–spin separation crossovers in small Hubbard nanoclusters

The exact numerical diagonalization and thermodynamics in an ensemble of small Hubbard clusters in the ground state and finite temperatures reveal intriguing insights into the nascent charge and spin pairings, Bose condensation and ferromagnetism in nanoclusters. The phase diagram off half filling strongly suggests the existence of quantum critical points and subsequent transitions from electron pairing into unsaturated and saturated ferromagnetic Mott–Hubbard like insulators, driven by electron repulsion. Rigorous criteria for the existence of quantum critical points and crossover temperatures are formulated. The phase diagram for 2×4$2\times 4$-site clusters illustrates how these features are scaled with cluster size. The phase separation and electron pairing, monitored by a magnetic field and electron doping, surprisingly resemble phase diagrams in the family of doped high-Tc$T_c$ cuprates.     

Single- and double-electron charge transfer in collisions of α-particles with hydrogen molecules

Total, partial, and angular differential cross sections of single- and double-electron charge transfer in collisions between α-particles and hydrogen molecules in the ground state in the interval of collision energies from 3 to 80 keV have been calculated. New data for charge transfer cross sections can be used for simulations and spectroscopy of α-particles in thermonuclear diverter plasma of nuclear reactors.     

On the zero fluctuation of the “microscopic free energy” and its potential use

The fluctuations of the microscopic free energy calculated with the ensemble probability are shown to be zero. We suggest that this result be used for estimating approximate free energies calculated on the basis of the minimum free energy principle. As an example the estimation is performed with respect to a certain computer simulation of the square Ising lattice. The zero fluctuations also can be used to obtain relations among fluctuations with the accurate ensemble probability distribution.     

On gravity’s role in the genesis of rest masses of classical fields

It is shown that in the Einstein-conformally coupled Higgs–Maxwell system with Friedman–Robertson–Walker symmetries the energy density of the Higgs field has stable local minimum only if the mean curvature of the \(t=\mathrm{const}\) hypersurfaces is less than a finite critical value \(\chi _c\), while for greater mean curvature the energy density is not bounded from below. Therefore, there are extreme gravitational situations in which even quasi-locally defined instantaneous vacuum states of the Higgs sector cannot exist, and hence one cannot at all define the rest mass of all the classical fields. On hypersurfaces with mean curvature less than \(\chi _c\) the energy density has the ‘wine bottle’ (rather than the familiar ‘Mexican hat’) shape, and the gauge field can get rest mass via the Brout–Englert–Higgs mechanism. The spacelike hypersurface with the critical mean curvature represents the moment of ‘genesis’ of rest masses.     

On the average electron–ion momentum transport cross-section in ideal and non-ideal plasmas

The energy-averaged electron–ion (e–i) momentum transport cross-section has been derived analytically and computed numerically. The result shows inaccuracy of the computations and fitting formula given by other authors.     

Structure of spin polarons in the t-t′ -t″ -Jz model

We calculate the Green function in the t-t '-t ”-J^z model and analyze the deformation of the quantum Néel state in the presence of a moving hole. Solving the problem in a self-consistent Born approximation and using Reiter's wave function we have found various spin correlation functions. We show that the different sign of hopping elements between the hole- and electron-doped system of high- cuprates is responsible for the sharp difference of the polaron structure between the two systems with antiferromagnetism stabilized in the electron-doped case by carriers moving mainly on one sublattice. Received 11 January 2000     

Enhanced molecular dynamics simulation of the transformation between α-helix and β-hairpin structures for peptide

ABSTRACT

Here, we investigated the secondary structure transformation for a design peptide, which has both the α-helix (PDB ID code 2DX3) and β-hairpin (PDB ID code 2DX4) structures in aqueous solution. We show that the transformation between α-helix and β-hairpin structures can be sampled efficiently using the enhanced sampling method based on integrated tempering without the definition of reaction coordinates. The reliable and smooth two-dimensional potential of mean force surfaces of the conformation space can be obtained efficiently, which has been used to propose the probable pathways for the transformation of the α-helix and β-hairpin structures. Our simulation results revealed the efficiency, and further suggested the general applicability of integrated tempering sampling method into complex biomolecule processes without prior structure knowledge.     

Calculation of the binding energy and of the parameters of low-energy scattering in the Λnp system

The cluster-reduction method is used to solve the differential Faddeev equations for S=1/2, T=0 and S=3/2, T=0 spin-isospin states of the Λnp system in the s-wave approximation. The NN interaction is simulated on the basis of the MT I–III potential model, and the ΛN potential is set to V _ΛN =V _NN /2. This simple option makes it possible to reproduce faithfully the binding energy of the hypertriton _Λ ³ H. The doublet and quadruplet Λd scattering lengths and the low-energy phase shifts are calculated. It is shown that the effective-range approximation is applicable to the cases of doublet and quadruplet scattering.     

Changes of properties of the soliton with temperature under influences of structure disorder in the α-helix protein molecules with three channels

The changes of property of solitons in α-helix protein molecules with three channels under influences of fluctuations of structure parameters and thermal perturbation of medium are extensively investigated using dynamic equations in the improved theory, numerical simulation and Runge-Kutta method. In this investigation the peculiarities of the solitons are given first in the motions of short-time and long-time and its collision features at T = 0 K and biological temperature T = 300 K. This study shows that the solutions of dynamic equations are solitons, which are very stable at T = 0 and 300 K, although its amplitudes and velocity are somewhat decreased relative to that at T = 0 K, the soliton can transport over 1000 amino acid residues, its lifetime is, at least, 120 ps. Subsequently, studies are made of the changes of properties of the soliton with variations of temperature of the medium and fluctuations of structure parameters including mass sequence of amino acid residues and the coupling constant, force constant, dipole–dipole interaction, chain–chain interaction and ground state energy in the α-helix proteins. The investigations indicate that the soliton has high thermal stability and can transport along the molecular chains retaining amplitude, energy and velocity, although the fluctuations of the structure parameters and temperature of the medium increase continually. However, the solitons disperse in larger fluctuations at T = 300 K and higher temperatures than 315 K. Thus it is determined that the critical temperature of the soliton is 315 K. Finally reasons are given for the generation of high thermal stability of the soliton and the correctness of the improved model is demonstrated. It is concluded that the soliton in the improved model is very robust against structure disorder and thermal perturbation of the α-helix protein molecules at 300 K, and is a possible carrier of bio-energy transport, and the improved model is maybe a candidate for the mechanism of this transport.