Structure and hydration of polycytidylic acid from the data of infrared spectroscopy, EHF dielectrometry and computer modeling

The aim of this paper is to summarize the original results concerned with the elucidation of the role of water environment in the formation of different structures of polyribocytidylic acid (poly(rC)), depending on the pH, temperature and ion content. To solve this problem, we studied the hydration of poly(rC)-K⁺ in films differing in water content, by methods of infrared spectroscopy and piezogravimetry, and in solution, using the dielectric measurements at a wavelength of 7.6 mm (extremely high frequencies — EHF). The experimental results were confirmed by a Monte Carlo simulation of the interaction between water molecules and single-strand and double-strand poly(rC) fragments in clusters of 800 water molecules. A model of hydration of double-strand complex of poly(rC)⁺-poly(rC) has been proposed based on our results and the known X-ray parameters of the complex. The obtained results and proposed structure of poly(rC)⁺-poly(rC) suggest that, the stabilization of this complex occurs due to intra- and inter-chain water bridges, together with the hydrogen bonds between neutral and protonated cytosines in pairs.     

Monte‐Carlo simulation of spatial distribution of characteristic x‐rays in multi‐film targets: source size of Al Kα x‐rays in W/Al film targets

A Monte‐Carlo simulation approach has been applied to describe the spatial distribution of characteristic x‐rays in W/Al film targets of different combinations of film thicknesses for the optimal design of a small‐sized x‐ray source having a high x‐ray intensity. The result has led to optimal combinations of W and Al film targets for 100 kV electrons, e.g. W(1 µm)/Al(20 µm), W(3 µm)/Al(15 µm) and W(5 µm)/Al(8 µm). These Al/W targets could be used as x‐ray sources for a medical instrument currently under development. Copyright © 2004 John Wiley & Sons, Ltd.     

DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water

Density functional theory (DFT) and Monte Carlo (MC) simulation with free energy perturbation (FEP) techniques have been used to study the tautomeric proton transfer reaction of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water. Two reaction pathways were considered: the direct and water-assisted transfers. The optimized structures and thermodynamic properties of stationary points for the title reaction system in the gas phase were calculated at the B3LYP/6-311+G(d, p) level of theory. The potential energy profiles along the minimum energy path in the gas phase and in water were obtained. The study of the solvent effect of water on the proton transfer of 2-amino-2-oxozoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline indicates that water as a solvent is favorable for the water-assisted process and slows down the rate of the direct transfer pathway.     

Dose prediction and process optimization in a gamma sterilization facility using 3-D Monte Carlo code

A model of a gamma sterilizer was built using the ITS/ACCEPT Monte Carlo code and verified through dosimetry. Individual dosimetry measurements in homogeneous material were pooled to represent larger bodies that could be simulated in a reasonable time. With the assumptions and simplifications described, dose predictions were within 2–5% of dosimetry. The model was used to simulate product movement through the sterilizer and to predict information useful for process optimization and facility design.     

流体熵相关性质的Monte Carlo模拟新方法

提出了用于计算实际体系熵相关性质的Monte Carlo多级取样分子模拟方法. 应用这一方法, 对硬球流体的化学势及Helmholtz自由能进行了估算, 得到了满意的结果. 计算化学势时, 不存在通常试验粒子方法所遇到的高密度问题. 该方法特别适合规律性的系统研究, 较之普通模拟方法要有效得多. 模拟得到的硬球体系无限稀释组份的超额化学势与对比直径的关系, 在相变区域为一条双凹曲线; 无论是在相变区还是在单相区, Carnahan-Starling公式对这一关系的描述均有较大偏差.     

Multistep methods for differential algebraic equations

Multistep methods for the differential/algebraic equations (DAEs) in the form of

The ground-state energy of the ±J sping glass. A comparison of various biologically motivated algorithms

We compare various evlutionary strategies to determine the ground-state energy of the ±J spin glass. We show that the choice of different evolution laws is less important than a suitable treatment of the free spins of the system At least one combination of these strategies does not give the correct results, but the ground states of the other different strategies coincide. Therefore we are able to extrapolate the infinit-size ground-state energy for the square lattice to –1.401±0.0015 and for the simple cubic lattice to –1.786±0.004.     

Critical exponents,hyperscaling, and universal amplitude ratios for two- and three-dimensional self-avoiding walks

We make a high-precision Monte Carlo study of two- and three-dimensional self-avoiding walks (SAWs) of length up to 80,000 steps, using the pivot algorithm and the Karp-Luby algorithm. We study the critical exponentsv and 2 ₄ – as well as several universal amplitude ratios; in particular, we make an extremely sensitive test of the hyperscaling relationdv = 2 ₄ –. In two dimensions, we confirm the predicted exponentv=3/4 and the hyperscaling relation; we estimate the universal ratios <R _g ² >/<R _e ² >=0.14026±0.00007, <R _m ² >/<R _e ² >=0.43961±0.00034, and ^*=0.66296±0.00043 (68% confidence limits). In three dimensions, we estimatev=0.5877±0.0006 with a correctionto-scaling exponent ₁=0.56±0.03 (subjective 68% confidence limits). This value forv agrees excellently with the field-theoretic renormalization-group prediction, but there is some discrepancy for ₁. Earlier Monte Carlo estimates ofv, which were 0.592, are now seen to be biased by corrections to scaling. We estimate the universal ratios <R _g ² >/<R _e ² >=0.1599±0.0002 and ^*=0.2471±0.0003; since ^*>0, hyperscaling holds. The approach to ^* is from above, contrary to the prediction of the two-parameter renormalization-group theory. We critically reexamine this theory, and explain where the error lies. In an appendix, we prove rigorously (modulo some standard scaling assumptions) the hyperscaling relationdv = 2 ₄ – for two-dimensional SAWs.     

Phase separation of symmetrical polymer mixtures in thin-film geometry

Monte Carlo simulations of the bond fluctuation model of symmetrical polymer blends confined between two neutral repulsive walls are presented for chain lengthN _A=N _B=32 and a wide range of film thicknessD (fromD=8 toD=48 in units of the lattice spacing). The critical temperaturesT _c (D) of unmixing are located by finite-size scaling methods, and it is shown that , wherev ₃0.63 is the correlation length exponent of the three-dimensional Ising model universality class. Contrary to this result, it is argued that the critical behavior of the films is ruled by two-dimensional exponents, e.g., the coexistence curve (difference in volume fraction of A-rich and A-poor phases) scales as , where ₂ is the critical exponent of the two-dimensional Ising universality class ( ₂=1/8). Since for largeD this asymptotic critical behavior is confined to an extremely narrow vicinity ofT _c (D), one observes in practice effective exponents which gradually cross over from ₂ to ₃ with increasing film thickness. This anomalous flattening of the coexistence curve should be observable experimentally.     

A goldstone mode in the Kawasaki-Ising model

The hydrodynamic regime of superfluids is dominated by a Goldstone mode corresponding to a spontaneously brokenU(1) symmetry. In this article we map the Kawasaki-Ising model for a classical lattice gas into a quantum model for a superfluid and establish a connection between the normal density fluctuations of the first and the Goldstone mode of the second. The fact that the quantum model we obtain describes a superfluid derives from an inequality by Penrose and Onsager which gives a lower bound to the Bose-Einstein condensate density. Mathematically, the Goldstone mode can be described by means of a quantum extension of the local algebra of the Ising model. The classification of its irreducible representations requires an additionalU(1) phase factor and the correspondingU(1) gauge symmetry is spontaneously broken for all finite values of the temperature and of the density.