Free-energy-based method for step size detection of processive molecular motors

We report a free-energy-based algorithm to estimate the step size of processive molecular motors from noisy, experimental time position traces. In our approach, the problem of estimating step sizes reduces to the evaluation of the free energy of directed lattice polymers in a random potential. The present approach is Bayesian in spirit as we do not aim to determine the most likely underlying time trace but rather to determine the step size and stepping frequency that are most likely to yield the observed data. We test this method on synthetic data for the simple case of noisy traces with fixed underlying step size and Poissonian stepping statistics. We find that the present scheme can work at signal-to-noise levels that are about 40% worse than those where the best existing step detection methods fail. More importantly, the present approach yields a much more accurate estimate of the step size. Although we focus on the case of non-reversing walks with a single step size, we show that we can detect if this assumption is violated. In principle, the method can be extended to more complex stepping scenarios but we find that for noisy data, multi-parameter fits are not reliable.     

A new formulation for the bethe approach to lattice statistics

An improved mathematical treatment is given for the approximate statistics of the Ising problem based on configurations of local Bethe clusters. The essential step in the development is to write the configuration probability for the Bethe cluster in terms of the probabilities for subclusters. Exact statistical mechanical results are used to interrelate the probabilities. The technique is illustrated first for a simple ferromagnetic lattice and then applied to the order-disorder problems of binary and ternary alloys on the face centered cubic lattice. In each ease the final equations which need solution are derived by strictly algebraic means. The improvement in mathematical treatment is such that these equations are identical with high order approximations of the very different cluster variation method.     

分步傅里叶法求解广义非线性薛定谔方程的改进及精度分析

利用分步傅里叶算法求解广义非线性薛定谔方程时对非线性项的处理往往采取了较多的数值近似,而且需要特别小心选择空间和时间的步长以及窗口尺寸,以保证精度要求.以描述光子晶体光纤中超连续谱产生的广义非线性薛定谔方程为例,利用分步傅里叶方法求解时对非线性项直接采用积分处理,而不采取任何数学近似,数值计算时又将积分变成卷积利用傅里叶变换求解,从而方便而又精确地完成了非线性项的计算.整个过程没有任何人为的近似,从而保证了计算模型的精确度.同时,还对因步长选择引起的计算精度进行了分析,提出了从频谱图上判断空间、时间步长选 关键词： 非线性光学 广义非线性薛定谔方程 分步傅里叶方法 超连续谱产生     

Tiling problems and undecidability in the cluster variation method

In cluster approximations for lattice systems the thermodynamic behavior of the infinite system is inferred from that of a relatively small, finite subsystem (cluster), approximations being made for the influence of the surrounding system. In this context we study, for translation-invariant classical lattice systems, the conditions under which a state for a cluster admits an extension to a global translation-invariant state. This extension problem is related to undecidable tiling problems. The implication is that restrictions of global translation-invariant states cannot be characterized purely locally in general. This means that there is an unavoidable element of uncertainty in the application of a cluster approximation.     

Impact of local attenuation approximations when estimating correlation length from backscattered ultrasound echoes

Estimating the characteristic correlation length of tissue microstructure from the backscattered power spectrum could improve the diagnostic capability of medical ultrasound. Previously, size estimates were obtained after compensating for source focusing, the frequency-dependent attenuation along the propagation path (total attenuation), and the frequency-dependent attenuation in the scattering region (local attenuation). In this study, the impact of approximations of the local attenuation on the scatterer size estimate was determined using computer simulations and theoretical analysis. The simulations used Gaussian impedance distributions with an effective radius of 25 microm randomly positioned in a homogeneous half-space sonified by a spherically focused source (f/1 to f/4). The approximations of the local attenuation that were assessed neglected local attenuation (i.e., assume 0 dB/cm-MHz) neglected frequency dependence of the local attenuation, and assumed a finite frequency dependence (i.e., 0.5 dB/cm-MHz) independent of the true attenuation of the medium. Errors in the scatterer size estimate due to the local attenuation approximations increased with increasing window length, increasing true local attenuation and increasing f number. The most robust estimates were obtained when the local attenuation was approximated by a tissue-independent attenuation value that was greater than 70% of the largest attenuation expected in the tissue region of interest.     

Calculation of the magnetization and total energy of vanadium as a function of lattice parameter

Self-consistent spin-polarized APW calculations have been performed to determine the energy band structure of metallic vanadium in an assumed ferromagnetic b.c.c. structure as a function of lattice parameter. The statistical exchange (‘Xα’) and muffin-tin approximations were used. At each lattice parameter for which a calculation was performed, the Xα cohesive energy, the pressure, and the magnetization were calculated. The calculated cohesive energy and pressure agree fairly well with experiment. The calculations also correctly predict the absence of a magnetic moment for vanadium at its equilibrium lattice constant. However, a nonmagnetic-to-magnetic transition is found to occur abruptly at a lattice constant which is about a factor of 1·25 larger than the equilibrium value, and which is in good qualitative agreement with the appearance of a local magnetic moment in certain vanadium alloys.     

Variational cluster approach to correlated electron systems in low dimensions

A self-energy-functional approach is applied to construct cluster approximations for correlated lattice models. It turns out that the cluster-perturbation theory [Phys. Rev. Lett. 84, 522 (2000)]] and the cellular dynamical mean-field theory [Phys. Rev. Lett. 87, 186401 (2001)]] are limiting cases of a more general cluster method. The results for the one-dimensional Hubbard model are discussed with regard to boundary conditions, bath degrees of freedom, and cluster size.     

On the many-body Van der Waals binding energy of a dense fluid

We consider a dense system of neutral atoms. When the atoms are represented by isotropic oscillators (Drude-Lorentz model) interacting with nonretarded dipole-dipole forces, the binding energy of the system is given exactly by a well-known expression which is written as a sum of two-bond, three-bond, etc., Van der Waals interactions. For a Bravais lattice this expression for the binding energy can be computed numerically to arbitrary accuracy. This has been done for the f.c.c. lattices of the noble-gas solids by Lucas. For a fluid an exact evaluation would require the knowledge of higher-order molecular distribution functions. Various approximations are discussed for this case, the simplest of which is the so-called long-wavelength approximation due to Doniach. When this approximation is checked by comparison with the exact result for a lattice, it turns out that the two-bond contribution leads to a value which is more than twice too large. Some more refined approximations are considered which treat the two-bond contribution exactly. It is pointed out that the model is consistent only if the distance of closest approach between the atoms is not too small.     

Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems

In this work we propose a hierarchy of Markov chain Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub-steps efficiently coupling coarse and finer state spaces. The method can be designed to sample the exact or controlled-error approximations of the target distribution, providing information on levels of different resolutions, as well as at the microscopic level. In both strategies the method achieves significant reduction of the computational cost compared to conventional Markov chain Monte Carlo methods. Applications in phase transition and pattern formation problems confirm the efficiency of the proposed methods.     

Expressing the Entropy of Lattice Systems as Sums of Conditional Entropies

Whether a system is to be considered complex or not depends on how one searches for correlations. We propose a general scheme for calculation of entropies in lattice systems that has high flexibility in how correlations are successively taken into account. Compared to the traditional approach for estimating the entropy density, in which successive approximations build on step-wise extensions of blocks of symbols, we show that one can take larger steps when collecting the statistics necessary to calculate the entropy density of the system. In one dimension this means that, instead of a single sweep over the system in which states are read sequentially, one take several sweeps with larger steps so that eventually the whole lattice is covered. This means that the information in correlations is captured in a different way, and in some situations this will lead to a considerably much faster convergence of the entropy density estimate as a function of the size of the configurations used in the estimate. The formalism is exemplified with both an example of a free energy minimisation scheme for the two-dimensional Ising model, and an example of increasingly complex spatial correlations generated by the time evolution of elementary cellular automaton rule 60.     

Quantum Lattice-Gas Model for the Burgers Equation

A quantum algorithm is presented for modeling the time evolution of a continuous field governed by the nonlinear Burgers equation in one spatial dimension. It is a microscopic-scale algorithm for a type-II quantum computer, a large lattice of small quantum computers interconnected in nearest neighbor fashion by classical communication channels. A formula for quantum state preparation is presented. The unitary evolution is governed by a conservative quantum gate applied to each node of the lattice independently. Following each quantum gate operation, ensemble measurements over independent microscopic realizations are made resulting in a finite-difference Boltzmann equation at the mesoscopic scale. The measured values are then used to re-prepare the quantum state and one time step is completed. The procedure of state preparation, quantum gate application, and ensemble measurement is continued ad infinitum. The Burgers equation is derived as an effective field theory governing the behavior of the quantum computer at its macroscopic scale where both the lattice cell size and the time step interval become infinitesimal. A numerical simulation of shock formation is carried out and agrees with the exact analytical solution.     

Molecular dynamic simulation of the size- and shape-dependent lattice parameter of small Platinum nanoparticles

The molecular dynamics simulation method has been used to study the size- and shape-dependent lattice parameter of unsupported small Pt nanoparticles, where the shapes concerned are sphere, cube, and cuboctahedron. It is shown that the lattice parameters decrease with decreasing the particle size in specific shape. The lattice variations of cubic shapes are higher than those of cuboctahedral shapes, and those of cuboctahedral shapes are higher than spherical ones. Furthermore, the shape effect on lattice parameter increases with decreasing the particle size. By linear fitting the simulated results, it is found that the particle shape can contribute to 7% of the total lattice parameter variation for cubic shape and to 5% for cuboctahedral shape. The present simulation results are qualitatively consistent with experimental values and the predictions by Continuous-Medium (CM) model.     

Lattice statistical aspects of electron correlation problems

A technique for the lattice statistics, the Kikuchi's cluster variation method, is applied to improve the Gutzwiller's method for the ground state problem of the many-electron system on the assumption that small number of macroscopic variables are enough to describe the feature of a whole configuration. The momentum distribution in the present approximation is no longer a step function consisting of two constant values, though some people might have been thinking that too simple distribution is an intrinsic weak point of the Gutzwiller's method. A metal-insulator transition of the Brinkman-Rice type takes place in the half-filled case also in the higher order approximations. The merit of the present scheme is in the realization of the correlated wavefunction rather than in the lowering of the ground state energy. Some spatial correlation functions are calculated. The role of the interaction range is studied.A part of this work was reported at the IUPAP International Conference on Statistical Physics held at Haifa, 24–30 August 1977On leave of absence from Department of Physics, Faculty of Science, Kyoto University, Kyoto 606, Japan     

Renormalized expansions for functional integrals: Generalized coherent potential approach to lattice models

An expansion for generating functionals (partition sums) of models expressed as lattice functional integrals with local (on-site) interactions is presented. This expansion renormalizes the standard perturbative expansion in such a way that certain its terms are summed up non-perturbatively. A non-self-consistent and a self-consistent versions of the expansion are formulated and criteria for an estimation of validity of approximations resulting from the both expansions are given. The simplest approximation being the first term of this expansion is applied to two lattice models: classicalN-component spin model and the model of non-interacting electrons in a disordered crystal. In the former model the critical temperature is calculated within 10% accuracy and in the latter, the coherent potential approximation is obtained.     

Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules

Shadow hybrid Monte Carlo (SHMC) is a new method for sampling the phase space of large molecules, particularly biological molecules. It improves sampling of hybrid Monte Carlo (HMC) by allowing larger time steps and system sizes in the molecular dynamics (MD) step. The acceptance rate of HMC decreases exponentially with increasing system size N or time step δt. This is due to discretization errors introduced by the numerical integrator. SHMC achieves an asymptotic O(N^1/4) speedup over HMC by sampling from all of phase space using high order approximations to a shadow or modified Hamiltonian exactly integrated by a symplectic MD integrator. SHMC satisfies microscopic reversibility and is a rigorous sampling method. SHMC requires extra storage, modest computational overhead, and a reweighting step to obtain averages from the canonical ensemble. This is validated by numerical experiments that compute observables for different molecules, ranging from a small n-alkane butane with four united atoms to a larger solvated protein with 14,281 atoms. In these experiments, SHMC achieves an order magnitude speedup in sampling efficiency for medium sized proteins. Sampling efficiency is measured by monitoring the rate at which different conformations of the molecules' dihedral angles are visited, and by computing ergodic measures of some observables.     

High precision mean-field results for lattice gauge theories: with special attention paid to the gauge dependence of mean-field perturbation theory to finite order

We do mean-field perturbation theory for U(1) lattice gauge theory in the axial gauge, and evaluate corrections from fluctuations up to fourth order for the free energy and plaquette energy. Comparing with similar results previously obtained in the Feynman gauge we find, to those orders studied, a gauge dependence of the size of the first correction term neglected with one exception. This gauge dependence decreases rapidly as the order of the approximation is increased. To any finite order, results in axial gauge are better approximations than results in the Feynman gauge. We speculate why. Assuming it to be generally true, we evaluate the first correction beyond the one-loop mean-field approximation to the free energy of SU(2) gauge theory with Wilson action in the axial gauge. This correction brings the mean-field result very close to Monte Carlo results for β > 1.6. It also makes the mean-field result identical, within a narrow margin, to ressumed strong coupling results in the interval 1.6 < β < 2.4, thus showing the absence of a phase transition.For both groups studied, we find that the asymptotic series of mean-field perturbation theory give much better approximations than do ordinary weak coupling series.     

Square lattice calculations for the general dimer and trimer problems using the Kikuchi method

Square lattice models for the general dimer and trimer problems are considered. A secondary lattice for the dimer problem is constructed, and a double square Kikuchi calculation produces an athermal molecular freedom within 2% of the known exact result. With interactions, departures from ideality of mixing entropy and vapour pressure are calculated at different temperatures, and an asymmetrical phase separation occurs at a reduced temperature 0.08. The general trimer problem is considered in a single square Kikuchi calculation. A single interaction is included. The molecular freedom and thermodynamic non-ideality of rigid linear, rigid angled and flexible trimers are compared. In the rigid linear case a phase separation occurs at reduced temperature 0.04. The molecular freedom of rigid linear trimers is calculated using higher Kikuchi approximations, and the result agrees well with previous estimates.     

A lattice Dirac operator for QCD with light dynamical quarks

In QCD chiral symmetry is explicitly broken by quark masses, the effect of which can be described reliably by chiral perturbation theory. Effects of explicit chiral symmetry breaking by the lattice regularisation of the Dirac operator, typically parametrised by the residual mass, should be negligible for almost all observables if the residual mass of the Dirac operator is much smaller than the quark mass. However, maintaining a small residual mass becomes increasingly expensive as the quark mass decreases towards the physical value and the continuum limit is approached. We investigate the feasibility of using a new approximately chiral Dirac operator with a small residual mass as an alternative to overlap and domain wall fermions for lattice simulations. Our Dirac operator is constructed from a Zolotarev rational approximation for the matrix sign function that is optimal for bulk modes of the hermitian kernel Dirac operator but not for the low-lying parts of its spectrum. We test our operator on various ³²³×64${32}^3\times 64$ lattices, comparing the residual mass and the performance of the Hybrid Monte Carlo algorithm at a similar lattice spacing and pion mass with a hyperbolic tangent operator as used by domain wall fermions. We find that our approximations have a significantly smaller residual mass than domain wall fermions at a similar computational cost, and still admit topological charge change.     

Approximations to wave propagation through a lattice of Dirichlet scatterers

A scheme of matched asymptotic expansions is used to obtain approximations to the dispersion relation when waves, governed by the Helmholtz equation, propagate through a two-dimensional lattice of scatterers on each of which a homogeneous Dirichlet boundary condition is imposed. The scatterers must be identical, but can be of any shape as long as each is small relative to the wavelength and the lattice periodicity. The results differ from those obtained using homogenisation in that there is no requirement that the wavelength be much longer than the lattice periodicity, and hence it is possible to describe band gaps.     

Optimizing magnetization orientation of permanent magnets for maximal gradient force

The force exercised on a permanent magnet (PM) in a nonuniform field (gradient force) is dependent on the magnetization orientation of the magnet. In this paper, it is shown theoretically that the gradient force is greatest when the magnetization through the magnet, or at least at its surface, is collinear with the external field. The formulae for calculating the force between an axis-symmetric optimal magnet and a coaxial axis-symmetric coil are presented. Using the finite element method (FEM), calculations of the magnetic field distribution of an optimal cylindrical magnet and some its approximations are performed. The forces between these magnets and a pancake coil are computed and compared. For a system consisting of a magnet with a height of 1 unit and a diameter of 2 units and magnetization invariant in field and an annular pancake coil with a diameter of 2.4 units, a thickness of 0.2 units, an inner diameter of 0.4 units and a distance from the magnet of 0.2 units, the force on the optimal magnet was 1.44 times greater than the force on an axially magnetized magnet of the same size and magnetization magnitude. The optimal magnetization may be approximated by magnetization inclined at a constant angle to the axis and by a combination of axially and radially magnetized sections. With magnetization at a constant angle to the axis in the axis plane, the force was greatest when the angle was about 45°, being 1.38-fold compared to the force on an axially magnetized magnet. When the magnet was composed of an axially magnetized cylindrical core and a radially magnetized outer ring, the force was greatest when the volume of the core was approximately equal to the volume of the ring, being 1.26-fold compared to the force on an axially magnetized magnet. The optimal magnet and its approximations also provided a reduced stray field. A short review of methods of the fabrication of permanent magnets (PMs) with a continuous variation of the magnetization orientation and with radial magnetization orientation is given.The results of this study can be used to design linear electromagnetic (micro)actuators.