Interaction of RNA molecules: Binding energy and the statistical properties of random sequences

The free binding energy of two RNA molecules is determined and some statistical properties such as fluctuation of the mean binding energy between two RNA molecules and the distribution of loop lengths in the structure formed are discussed. An analysis of the dependence of the specific free energy of a complex of two long random RNA molecules on the number c of nucleotide types led us to suggest that the four-letter genetic alphabet used by nature plays a special role.     

Theoretical study of molecular ordering in liquid crystals with the help of intermolecular interaction energy calculations

A theoretical analysis has been carried out to determine the molecular alignment of some nematic liquid crystals like DPAB (4, 4'-di-n-propoxy-azoxybenzene), EPAB (ethyl para-azoxybenzoate) and PAA (para-azoxyanisole). CNDO/2 method has been employed to evaluate the net atomic charge and atomic dipole components at each atomic centre of the molecules. Configurational energy has been computed using a modified Rayleigh-Schrodinger perturbation method at an interval of 1 Å in translation and 10° in rotation between a pair of DPAB molecules. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible geometrical arrangements between a molecular pair have been considered. A comparative picture of molecular parameters like total energy, binding energy, total dipole moment etc., has been obtained. An attempt has been made to explain the nematogenic behaviour of liquid crystal and thereby develop a molecular model for liquid crystallinity.     

Molecular alignment of biphenyl derivatives -a computational analysis

Molecular alignment of some biphenyl derivatives likes 4'-Nitro-2-biphenylamine (NBPA), 4-Acetyl-3'-chlorobiphenyl (ACBP) and 4-Acetyl-3'-florobiphenyl (AFBP) has been examined. The CNDO/2 method has been employed to compute the net atomic charge and atomic dipole-moment components at each atomic centre. Configurational energy has been computed using a modified Rayleigh- Schrodinger perturbation method at an interval of 0.1 A° in translation and 1° in rotation, and corresponding probabilities have been calculated using MB-statistics. A comparative study of molecular parameters like the total energy, the binding energy and the total dipole moment etc., has been made. On the basis of the stacking and the in-plane interaction energy calculations, all the possible geometrical arrangements between molecular pairing have been obtained. The investigation suggests that a strong intermolecular interaction energy between a pair of NBPA molecules, and the specific minimum energy configuration, determines the alignment of molecules with respect to one another. An attempt has been made to correlate the liquid crystalline properties exhibited by this class of molecules, and thereby develop a molecular model for the liquid crystallinity.     

Theory of polar fluids. I

We examine a classical fluid composed of molecules which contain a polarizable electric dipole with finite permanent moment. The long-ranged dipolar and the short-ranged interactions are treated on a different footing by expanding relative to a reference system characterized by the absence of electrostatic interactions. Extensions of graph theoretical techniques developed in an earlier paper are used to analyse the pair distribution function and the dielectric constant. Reduction of the number of graphs and their complexity is effected by introducing renormalizations of the permanent moment and the polarizability. The analysis leads to the definition of a new function w(12), which is free of terms dependent on the shape of the sample. For polar, polarizable molecules the direct correlation function lacks translational invariance; its role as a basic quantity is ceded to w(12). The pair distribution function and the dielectric constant ε are expressed in terms of w(12) and two closely related functions. Attention is drawn to an unsolved problem in dielectric theory, and an alternative formula for ε is presented in the form of a conjecture. An approximation for ε is formulated for the case in which the short-ranged non-dipolar interactions are independent of the molecular orientations. A simplified version is solved analytically.     

A Variational Wave Function for 2p2-Orbitals in Atomic Negative Ions

A variational wave function is used to describe the binding energy of atomic negative ions using a two-electron system in the 2p²-state. Each electron is described by a modified screened hydrogenic wave function involving two free screening parameters denoted by c and a. The model is applied to hydrogen, helium, lithium, and boron anions, where the optimum values of the screening parameters are deduced through fitting the optimized energy to available experimental and theoretical values. The behavior of the optimum wave function for each anion is also investigated as a function of electronic radial distance and compared with its counterpart in the screened hydrogenic model and the Hartree–Fock method.     

Do electrons change their c-axis kinetic energy upon entering the superconducting state?

The interlayer tunneling mechanism of the cuprate high temperature superconductors involves a conversion of the confinement kinetic energy of the electrons perpendicular to the CuO-planes (c-axis) in the normal state to the pair binding energy in the superconducting state. This mechanism is discussed and the arguments are presented from the point of view of general principles. It is shown that recent measurements of the c-axis properties support the idea that the electrons substantially lower their c-axis kinetic energy upon entering the superconducting state, a change that is nearly impossible in any conventional mechanism. The proper use of a c-axis conductivity sum rule is shown to resolve puzzles involving the penetration depth and the optical measurements. Received: 5 January 1998 / Accepted: 17 March 1998     

Phase transition of directed polymer in random potentials on 4+1 dimensions

Finite-temperature-directed polymer in random potentials is described by a transfer matrix method. On 4+1 dimensions, the evidence for a finite-temperature phase transition is found at T_c≈0.18, where the free energy fluctuation grows logarithmically as a function of time t. When TT_c, the fluctuation of the free energy grows as t^ω with ω≈0.156. The phase transition of the restricted solid-on-solid model, which is closely related to the directed polymer problem through the Kardar–Parisi–Zhang equation, is also discussed.     

Intermolecular interaction effect on the line-shape of hyper-Rayleigh light scattering by molecular liquids

Scattering on molecules, correlated in regions of short-range quasi-ordering, is analysed with regard to its effect on the spectrum of hyper-Rayleigh light-scattering by molecular liquids. The general form of S ^2ω _c(?, Δω) derived using spherical tensors and expanding the orientational-positional-time pair correlation function in Wigner functions, is discussed on the assumption that Vineyard's [22] approximation can be applied to calculate G _c[τ₁(t), τ₂(0)]. Successive terms of the expansion are calculated assuming dipole-dipole interaction energy as predominant in the total molecular electric multipole interaction energy. In the present approximation the contribution from scattering on correlated molecules is shown to be given by the difference of two Lorentz lines, whose maxima depend on the magnitude of the interactions. The integral intensities, calculated from the formulae derived here, are in agreement with those of the literature.     

Molecular dynamic simulation of the thermodynamic and kinetic properties of nucleotide base pair

A nucleotide base pair is the basic unit of RNA structures. Understanding the thermodynamic and kinetic properties of the closing and opening of a base pair is vital for quantitative understanding the biological functions of many RNA molecules. Due to the fast transition rate, it is difficult to directly observe opening and closing of single nucleic acid base pair in experiments. This review will provide a brief summary of the studies about the thermodynamic and kinetic properties of a base pair opening and closing by using molecular dynamic simulation methods.     

On the short range magnetic order of iron aboveT c

A derivation of the ordering part of the free energy functional based on an expansion about the free energy of a random CPA tight-binding paramagnetic effective medium is presented. Considering the dominant term of this functional, which is of Heisenberg form, the static magnetic correlation function is calculated within a spherical model approximation. For some parameters a behaviour characteristics for systems with tendency to form helicoidal ordered structure belowT _c is observed.     

Statistical thermodynamics of isolated rigid rod-like molecules near a surface

The configurational behaviour and thermodynamic properties of a dilute gas of rigid rod-like molecules in the vicinity of a macroscopic planar adsorption surface are investigated using statistical mechanics. The interaction energy between the surface and a rod-like molecule is determined as a function of both its molecular centre of mass separation R and its orientation relative to the surface. In calculating this interaction energy, each rod segment and molecule comprising the surface is assumed to interact through a Lennard-Jones pair potential. The average molecular order parameter is then determined as a function of R. We find that an isolated rod-like molecule tends to align nearly parallel to the surface for small separations. However, as R increases the order parameter first passes through a maximum then decays to zero as R ^-5 for large R. The configurational behaviour of an isolated rod-like molecule located between two parallel adsorption surfaces is also considered briefly. The surface spreading pressure, excess surface energy and entropy are also obtained for a dilute gas of rod-like molecules near a surface. We find that the extent of surface binding increases nearly exponentially with molecular length at constant temperature and surface density, and that the excess surface energy and entropy are essentially proportional to the molecular length.     

Perturbative solution to order βɛ of the Percus-Yevick equation for triangular well potential forn=2

The radial distribution function for a fluid in which the molecules interactvia a triangular well potential is considered. Expanding the radial distribution function in pwoers of βɛ, where ɛ is the depth of the potential andβ=1/k _BT the first-order terms are calculated analytically using the Percus-Yevick theory in the Baxter’s formulation. The first-order terms in the direct correlation functionc(r) are also calculated. The first- and second-order terms in the free energy obtained from the energy equation of state are calculated and compared with other calculations. An erratum to this article is available at .     

Statistical theory of the elastic constants of nematic liquid crystals

A statistical mechanical theory of the Frank elastic constants is formulated. The free energy functional is constructed for the deformed sample and the free energy density is defined for the case of small spatial gradients. The Frank constants are expressed in terms of the direct correlation function c(1, 2) and the orientational single particle distribution function. For the example of Onsager spherocylinders three constants K ₁, K ₂ and K ₃ are calculated. The results of these calculations are similar to those given by Priest and by Straley.     

On the fast-time oscillatory instabilities of Liñán's diffusion-flame regime

Fast-time instability for diffusion flames, with Lewis numbers set equal for fuel and oxidizer but greater than unity, is numerically analysed by the activation energy asymptotics and Evans function method. The time and length scales being chosen to be those of the inner reactive–diffusive layer, the problem corresponds to the instability problem for the Liñán's diffusion-flame regime. The instability is primarily oscillatory and emerges prior to reaching the turning point of the characteristic C-curve, usually known as the Liñán's extinction condition. A critical Lewis number, L _c , is also found, across which the instability changes its qualitative character. Below L _c , the instability possesses primarily a pulsating nature in that the two real branches of the dispersion relation existing for small wave numbers merge at a finite wave number, from which a pair of complex conjugate branches bifurcate. The maximum growth rate is found at the zero wave number. For Lewis numbers greater than L _c , the eigensolution branch for small reactant leakages is found to be purely complex with the maximum growth rate found at a finite wave number, thereby exhibiting a travelling nature. As the reactant-leakage parameter is further increased, the instability characteristics turns into a pulsating type, similar to that for 1 < L < L _c . The switching between different instability characters is found to correspond to the Bogdanov-Takens bifurcation.     

Molecular dynamics of liquid alkaline-earth metals near the melting point

Results of the studies of the properties like binding energy, the pair distribution function g(r), the structure factor S(q), specific heat at constant volume, velocity autocorrelation function (VACF), radial distribution function, self-diffusion coefficient and coordination number of alkaline-earth metals (Be, Mg, Ca, Sr and Ba) near melting point using molecular dynamics (MD) simulation technique using a pseudopotential proposed by us are presented in this article. Good agreement with the experiment is achieved for the binding energy, pair distribution function and structure factor, and these results compare favourably with the results obtained by other such calculations, showing the transferability of the pseudopotential used from solid to liquid environment in the case of alkaline-earth metals.     

Dissociation and dissociative phase transition in dense hydrogen

A simple physical model is proposed for dissociating dense fluid hydrogen. We propose that free dissociated atoms interact via quantum electron-electron exchange analogously to the interaction in the liquid-metal phase of alkali metals. The density dependence of a hydrogen atom’s binding energy in such a quasi-liquid is calculated. It is shown that the transition from the molecular fluid to liquid hydrogen is a first-order phase transition. The critical parameters of the transition are determined: P _c = 72 GPa, T _c = 10500 K, and ρ _c = 0.5 g/cm³. The possibility of the metastable existence of atomic liquid hydrogen in a dissociated molecular fluid under decreased pressure is established.     

Vertex cover problem studied by cavity method: Analytics and population dynamics

We study the vertex cover problem on finite connectivity random graphs by zero-temperature cavity method. The minimum vertex cover corresponds to the ground state(s) of a proposed Ising spin model. When the connectivity c > e = 2.718282, there is no state for this system as the reweighting parameter y, which takes a similar role as the inverse temperature β in conventional statistical physics, approaches infinity; consequently the ground state energy is obtained at a finite value of y when the free energy function attains its maximum value. The minimum vertex cover size at given c is estimated using population dynamics and compared with known rigorous bounds and numerical results. The backbone size is also calculated. Received 11 November 2002 Published online 1st April 2003 RID="a" ID="a"e-mail: zhou@mpikg-golm.mpg.de     

Theory of tensor invariants of integrable Hamiltonian systems. I. Incompatible Poisson structures

This paper develops a new theory of tensor invariants of a completely integrable non-degenerate Hamiltonian system on a smooth manifoldM ⁿ. The central objects in this theory are supplementary invariant Poisson structuresP _c which are incompatable with the original Poisson structureP ₁ for this Hamiltonian system. A complete classification of invariant Poisson structures is derived in a neighbourhood of an invariant toroidal domain. This classification resolves the well-known Inverse Problem that was brought into prominence by Magri's 1978 paper deveoted to the theory of compatible Poisson structures. Applications connected with the KAM theory, with the Kepler problem, with the basic integrable problem of celestial mechanics, and with the harmonic oscillator are pointed out. A cohomology is defined for dynamical systems on smooth manifolds. The physically motivated concepts of dynamical compatibility and strong dynamical compatibility of pairs of Poisson structures are introduced to study the diversity of pairs of Poisson structures incompatible in Magri's sense. It is proved that if a dynamical systemV preserves two strongly dynamically compatible Poisson structuresP ₁ andP ₂ in a general position then this system is completely integrable. Such a systemV generates a hierarchy of integrable dynamical systems which in general are not Hamiltonian neither with respect toP ₁ nor with respect toP ₂. Necessary conditions for dynamical compatibility and for strong dynamical compatibility are derived which connect these global properties with new local invariants of an arbitrary pair of incompatible Poisson structures.Supported by NSERC grant OGPIN 337.     

Study of the solid-liquid-vapour phase equilibria of flexible chain molecules using Wertheim's thermodynamic perturbation theory

The phase diagram of flexible molecules formed by freely-jointed tangent spheres is studied using the first-order thermodynamic perturbation theory of Wertheim for both fluid and solid phases. A mean-field term is added to the free energy of the fluid and solid phase in order to account for attractive dispersion forces. The approach is used to determine the global (solid-liquid-vapour) phase diagrams and triple points of chain molecules of increasing chain length. It is found that the triple point temperature is not affected strongly by the length of the chain, whereas the gas-liquid critical temperature increases dramatically. The asymptotic limits of the phase diagram for infinitely long chains are discussed. The reduced critical temperature of infinitely long chains as given by the mean-field theory is 2/3, and the reduced triple point temperature is 0.048 56, so that an asymptotic value of T _t/T _c = 0.07284 for the ratio of the triple to critical point temperatures is obtained. This indicates that fully-flexible tangent chains present an enormous liquid range. The proposed theory, while being extremely simple, provides a useful insight into the phase behaviour of chain molecules, showing the existence of finite asymptotic limits for the triple and critical point temperatures. However, since n-alkanes present an asymptotic limit of about T _t/T _c, = 0.40, the agreement With experiment is not quantitative. This suggests that fully flexible models may not be appropriate to model the solid phases of real chain molecules.     

Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: Implications for DNA hybridization

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy —c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low-temperature/low-force compact (folded) structure and a high-temperature/high-force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c ≲ 2.479 a melting transition is possible; for c ≤ 2 the chain is always in the folded phase and for 2.479 ≲ c always in the unfolded phase. A force-induced melting transition with singular behavior is possible for all loop exponents c < 2.479 and can be observed experimentally by single-molecule force spectroscopy. These findings have implications for the hybridization or denaturation of double-stranded nucleic acids. The Poland-Scheraga model for nucleic acid duplex melting does not allow base pairing between nucleotides on the same strand in denatured regions of the double strand. If the sequence allows these intra-strand base pairs, we show that for a realistic loop exponent c ≈ 2.1 pronounced secondary structures appear inside the single strands. This leads to a lower melting temperature of the duplex than predicted by the Poland-Scheraga model. Further, these secondary structures renormalize the effective loop exponent [^(c)] \hat{{c}}, which characterizes the weight of a denatured region of the double strand, and thus affect universal aspects of the duplex melting transition.