A new algorithm for the fixed-node quantum Monte Carlo method

A novel algorithm is proposed for the fixed-node quantum Monte Carlo (FNQMC) method.In contrast to previous procedures,its "guiding function" is not optimized prior to diffusion quantum Monte Carlo (DMC) computation but synchronistically in the diffusion process The new algorithm can not only save CPU time,but also make both of the optimization and diffusion carried out according to the same sampling fashion,reaching the goal to improve each other This new optimizing procedure converges super-linearly,and thus can accelerate the particle diffusion During the diffusion process,the node of the "guiding function" changes incessantly,which is conducible to reducing the "fixed-node error" The new algorithm has been used to calculate the total energies of states X3B1 and a1A1 of CH2 as well as π-X2B1 and λ-2A1 of NH2 The singlet-triplet energy splitting (λEsT) in CH2 and π energy splitting in NH2 obtained with this present method are (45 542±1.840) and (141.644±1.589) kJ/mol,respectively The calculated     

Monte Carlo Simulation of the Assembly of bis‐Biotinylated DNA and Streptavidin

We present Monte Carlo simulations of the self‐assembly of bivalent bis‐biotinylated DNA molecules with the tetravalent biotin‐binding protein streptavidin (STV). By fitting the STV binding probabilities for the four possible valencies, the modelling correctly reproduces the dependencies of various network parameters experimentally observed in an earlier study. The combined results from the experimental and theoretical studies suggest that the binding probability for divalent STV formation is about 50 times larger than for the formation of trivalent and about 200 times larger than for tetravalent STV. In accordance with the experimental results, the modelling also indicates that the mixture of an equimolar ratio of DNA and STV leads to a maximum in size of the oligomeric DNA–STV clusters formed. Furthermore, we found a percolation transition in which the DNA cluster size increases rapidly with increasing DNA concentration resulting in the formation of a single supercluster at elevated concentrations. This behaviour coincides with the occurrence of an immobile band previously observed in electrophoretic experiments, indicating the formation of extremely large DNA–STV aggregate networks.     

Monte Carlo simulation of polarizable systems: Early rejection scheme for improving the performance of adiabatic nuclear and electronic sampling Monte Carlo simulations

An early rejection scheme for trial moves in adiabatic nuclear and electronic sampling Monte Carlo simulation (ANES-MC) of polarizable intermolecular potential models is presented. The proposed algorithm is based on Swendsen–Wang filter functions for prediction of success or failure of trial moves in Monte Carlo simulations. The goal was to reduce the amount of calculations involved in ANES-MC electronic moves, by foreseeing the success of an attempt before making those moves. The new method was employed in Gibbs ensemble Monte Carlo (GEMC) simulations of the polarizable simple point charge-fluctuating charge (SPC-FQ) model of water. The overall improvement in GEMC depends on the number of swap attempts (transfer molecules between phases) in one Monte Carlo cycle. The proposed method allows this number to increase, enhancing the chemical potential equalization. For a system with 300 SPC-FQ water molecules, for example, the fractions of early rejected transfers were about 0.9998 and 0.9994 at 373 and 423 K, respectively. This means that the transfer moves consume only a very small part of the overall computing effort, making GEMC almost equivalent to a simulation in the canonical ensemble.     

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.     

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.