A Simulated Annealing Algorithm for Training Empirical Potential Functions of Protein Folding

In this paper are reported the local minimum problem by means of current greedy algorithm for training the empirical potential function of protein folding on 8623 non-native structures of 31 globular proteins and a solution of the problem based upon the simulated annealing algorithm. This simulated annealing algorithm is indispensable for developing and testing highly refined empirical potential functions.

Lyapunov function as potential function: A dynamical equivalence

For a physical system, regardless of time reversal symmetry, a potential function serves also as a Lyapunov function, providing convergence and stability information. In this paper, the converse is constructively proved that any dynamics with a Lyapunov function has a corresponding physical realization： a friction force, a Lorentz force, and a potential function. Such construction establishes a set of equations with physical meaning for Lyapunov function and suggests new approaches on the significant unsolved problem namely to construct Lyapunov functions for general nonlinear systems. In addition, a connection is found that the Lyapunov equation is a reduced form of a generalized Einstein relation for linear systems, revealing further insights of the construction.

Nonlinear dynamics and performance analysis of modified snap-through vibration energy harvester with time-varying potential function

Vibration energy harvesting has emerged as a promising method to harvest energy for small-scale applications.Enhancing the performance of a vibration energy harvester(VEH)incorporating nonlinear techniques,for example,the snap-through VEH with geometric non-linearity,has gained attention in recent years.A conventional snap-through VEH is a bi-stable system with a time-invariant potential function,which was investigated extensively in the past.In this work,a modified snap-through VEH with a time-varying potential function subject to harmonic and random base excitations is investigated.Modified snap-through VEHs,such as the one considered in this study,are used in wave energy harvesters.However,the studies on their dynamics and energy harvesting under harmonic and random excitations are limited.The dynamics of the modified snap-through VEH is represented by a system of differential algebraic equations(DAEs),and the numerical schemes are proposed for its solutions.Under a harmonic excitation,the system exhibits periodic and chaotic motions,and the energy harvesting is superior compared with the conventional counterpart.The dynamics under a random excitation is investigated by the moment differential method and the numerical scheme based on the modified Euler-Maruyama method.The Fokker-Planck equation representing the dynamics is derived,and the marginal and joint probability density functions(PDFs)are obtained by the Monte Carlo simulation.The study shows that the modified snap-through oscillator based VEH performs better under both harmonic and random excitations.The dynamics of the system under stochastic resonance(SR)is investigated,and performance enhancement is observed.The results from this study will help in the development of adaptive VEH techniques in the future.

A Global Minimization Algorithm for Empirical Contact Potential Functions

Global minimization algorithm is indispensable to solving the protein folding problem based upon thermodynamic hypothesis. Here we propose a pseudo potential function, contact difference(CD), for simulating empirical contact potential functions and testing global minimization algorithm. The present paper covers conformational sampling and global minimization algorithm called BML03, based upon Monte Carlo and simulated annealing, which is able to locate CD′s global minimum and refold extended protein structures into ones with root mean square distance(RMSD) as small as 0.03 nm from the native structures. For empirical contact potential functions, these results demonstrate that their global minimization problems may be solvable.

A Global Minimization Algorithm for Empirical Contact Potential Functions

Global minimization algorithm is indispensable for solving protein folding problems based on thermodynamic hypothesis. A contact difference （CD） based on pseudo potential function, for simulating empirical contact potential functions and testing global minimization algorithm was proposed. The present article describes a conformational sampiing and global minimization algorithm, which is called WL, based on Monte Carlo simulation and simulated annealing. It can be used to locate CD＇s globe minimum and refold extended protein structures, as small as 0. 03 nm, from the native structures, back to ones with root mean square distance（RMSD）. These results demonstrate that the global minimization problems for empirical contact potential functions may be solvable.

Effects of potential functions on stochastic resonance

In this paper, the effects of a bistable potential function U（x） = -ax2/2＋b｜x＋｜2y/（2y） on stochastic resonance （SR） is discussed. We investigate the effects of index y on the performance of the SR system with fixed parameters a and b, and with fixed potential barriers, respectively. To measure the performance of the SR system in the presence of an aperiodic input, the bit error rate is employed, as is commonly used in binary communications. The numerical simulations strongly support the theoretical results. The goal of this investigation is to explore the effects of the shape of potential functions on SR and give a guidance of nonlinear systems in the application of information processing.

Scaling for Experimental Inner-Sphere Reorganization Energy of Hydrated Ions via Accurate Potential Function

Reported here are several new calculation methods for the inner-sphere reorganization energy of hydrated metal ions involved in electron transfer processes.It is based on the self-exchange model of reorganization and utilizes the more exact potential functions between central metal ion and the inner-sphere ligands.The parameters involved are determined via the spectroscopic and thermodynamic data.The predictions of the inner-sphere reorganization energies from those models agree well with the photoemission experimental results.

Review of Proposed Stress-dilatancy Relationships and Plastic Potential Functions for Uncemented and Cemented Sands

Stress-dilatancy relationship or plastic potential function are crucial components of every elastoplastic constitutive model developed for sand or cemented sand.This is because the associated flow rule usually does not produce acceptable outcomes for sand or cemented sand.Many formulas have been introduced based on the experimental observations in conventional and advanced plasticity models in order to capture ratio of plastic volumetric strain increment to plastic deviatoric strain increment(i.e.dilatancy rate).Lack of an article that gathers these formulas is clear in the literature.Thus,this paper is an attempt to summarize plastic potentials and specially stress-dilatancy relations so far proposed for constitutive modelling of cohesionless and cemented sands.Stress-dilatancy relation is usually not the same under compression and extension conditions.Furthermore,it may also be different under loading and unloading conditions.Therefore,the focus in this paper mainly places on the proposed stress-dilatancy relations for compressive monotonic loading.Moreover because plastic potential function can be calculated by integration of stress-dilatancy relationship,more weight is allocated to stress-dilatancy relationship in this research.

New Method on Constructing Analytic Potential Function of Diatomic Molecules

A new method on constructing analytical potential energy functions is presented, and then a relatively universal analytical potential energy function for precisely calculating the spectra of ＇iatomic molecules and ions is derived. Furthermore, six kinds of common potential energy curves containing three main potential curves i,e. steady state, metastable state and repulsive state are obtained from this potential energy function. Finally, spectroscopic parameters of thirteen diatomic molecules and ions including BeD-X^2∑＋, BeT-X^2∑^＋ and Na2-X^1∑g^＋ etc are calculated by using the potential function, as a consequence, all calculation results are in good agreement with experimental data.

Molecular properties and potential energy function model of BH under external electric field

Using the density functional B3P86/cc-PV5Z method, the geometric structure of BH molecule under different external electric fields is optimized, and the bond lengths, dipole moments, vibration frequencies, and other physical properties parameters are obtained. On the basis of setting appropriate parameters, scanning single point energies are obtained by the same method and the potential energy curves under different external fields are also obtained. These results show that the physical property parameters and potential energy curves may change with external electric field, especially in the case of reverse direction electric field. The potential energy function without external electric field is fitted by Morse potential, and the fitting parameters are obtained which are in good agreement with experimental values. In order to obtain the critical dissociation electric parameter, the dipole approximation is adopted to construct a potential model fitting the corresponding potential energy curve of the external electric field. It is found that the fitted critical dissociation electric parameter is consistent with numerical calculation, so that the constructed model is reliable and accurate. These results will provide important theoretical and experimental reference for further studying the molecular spectrum, dynamics, and molecular cooling with Stark effect.

Reconstructing the Potential Function in a Formulation of Quantum Mechanics Based on Orthogonal Polynomials

In a recent reformulation of quantum mechanics, the properties of the physical system are derived from orthogonal polynomials that make up the expansion coefficients of the wavefunction in a complete set of square integrable basis. Here, we show how to reconstruct the potential function so that a correspondence with the standard formulation could be established. However, the correspondence places restriction on the kinematics of such problems.

Spacecraft formation reconfiguration with multi-obstacle avoidance under navigation and control uncertainties using adaptive artificial potential function method

In this paper,an adaptive artificial potential function(AAPF)method is developed for spacecraft formation reconfiguration with multi-obstacle avoidance under navigation and control uncertainties.Furthermore,an improved Linear Quadratic Regular(ILQR)is proposed to track the reference trajectory and a Lyapunov-based method is employed to demonstrate the stability of the overall closed-loop system.Compared with the traditional APF method and the equal-collision-probability surface(ECPS)method,the AAPF method not only retains the advantages of APF method and ECPS method,such as low computational complexity,simple analytical control law and easy analytical validation progress,but also proposes a new APF to solve multi-obstacle avoidance problem considering the influence of the uncertainties.Moreover,the ILQR controller obtains high control accuracy to enhance the safe performance of the spacecraft formation reconfiguration.Finally,the effectiveness of the proposed AAPF method and the ILQR controller are verified by numerical simulations.

On Conway's Potential Function for Colored Links

The Conway potential function （CPF） for colored links is a convenient version of the multi- variable Alexander-Conway polynomial. We give a skein characterization of CPF, much simpler than the one by Murakami. In particular, Conway＇s ＂smoothing of crossings＂ is not in the axioms. The proof uses a reduction scheme in a twisted group-algebra PnBn, where Bn is a braid group and Pn is a domain of multi-variable rational fractions. The proof does not use computer algebra tools. An interesting by-product is a characterization of the Alexander-Conway polynomial of knots.

Analytical potential energy function for the electronic states ~2Π_(1/2) and ~2Π_(3/2) of O_2~x (x=+1,-1)

The splitting of potential energy levels for ground state X^2∏g of O^x2 （x = ＋1,-1） under spin-orbit coupling （SOC） has been calculated by using the spin-orbit （SO） multi-configuration quasi-degenerate perturbation theory （SO-MCQDPT）. Their Murrell-Sorbie （M S） potential functions are gained, and then the spectroscopic constants for electronic states 2^∏1/2 and 2^∏3/2 are derived from the M S function. The vertical excitation energies for O^x2 （x = ＋1,-1） are v[O2＋1^（2∏3/2→X^2∏1/2）] =195.652cm^-1, and v[O2^-1（2^∏1/2 →X^2∏3/2）] =182.568cm^-1, respectively. All the spectroscopic data for electronic states 2^∏1/2 and 2^∏3/2 are given for the first time.

A UNIVERSAL ANALYTIC POTENTIAL-ENERGY FUNCTION BASED ON A PHASE FACTOR

Using a field equation with a phase factor, a universal analytic potential-energy function applied to the interactions between diatoms or molecules is derived, and five kinds of potential curves of common shapes are obtained adjusting the phase factors. The linear thermal expansion coefficients and Young's moduli of eleven kinds of face-centered cubic (fcc) metals - Al, Cu, Ag, etc. are calculated using the potential-energy function; the computational results are quite consistent with experimental values. Moreover, an analytic relation between the linear thermal expansion coefficients and Young's moduli of fcc metals is given using the potential-energy function. Finally, the force constants of fifty-five kinds of diatomic moleculars with low excitation state are computed using this theory, and they are quite consistent with RKR (Rydberg-Klein-Rees) experimental values.

Structure and analytical potential energy function for the ground state of the BC^x （x=0, -1）

In this paper, the electronic states of the ground states and dissociation limits of BC and BC- are correctly determined based on group theory and atomic and molecular reaction statics. The equilibrium geometries, harmonic frequencies and dissociation energies of the ground state of BC and BC- are calculated by using density function theory and quadratic CI method including single and double substitutions. The analytical potential energy functions of these states have been fitted with Murrell-Sorbie potential energy function from our ab initio calculation results. The spectroscopic data （αe, ωe and ωeχe） of each state is calculated via the relation between analytical potential energy function and spectroscopic data. All the calculations are in good agreement with the experimental data.

Ab initio calculations of accurate dissociation energy and analytic potential energy function for the second excited state B^1∏ of ^7LiH

The reasonable dissociation limit of the second excited singlet state B1∏ of ^7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B^∏ state are calculated using a symmetry-adaptedcluster configuration interaction method in full active space. The whole potential energy curve for the B1H state is obtained over the internuclear distance ranging from about 0.10 nm to 0,54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B^1∏ state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B^1∏ state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.

The Analytical Potential Energy Function of NH Radical Molecule in External Electric Field

The geometric structures of an Nit radical in different external electric fields are optimized by using the density functional B3P86/cc-PVSZ method, and the bond lengths, dipole moments, vibration frequencies and IR spectrum are obtained. The potential energy curves are gained by the CCSD （T） method with the same basis set. These results indicate that the physical property parameters and potential energy curves may change with the external electric field, especially in the reverse direction electric field. The potential energy function of zero field is fitted by the Morse potential, and the fitting parameters are in good accordance with the experimental data. The potential energy functions of different external electric fields are fitted adopting the constructed potential model. The fitted critical dissociation electric parameters are shown to be consistent with the numerical calculation, and the relative errors are only 0.27% and 6.61%, hence the constructed model is reliable and accurate. The present results provide an important reference for further study of the molecular spectrum, dynamics and molecular cooling with Stark effect.

Ab initio calculation on accurate analytic potential energy functions and harmonic frequencies of c^3∑g^＋ and B^1-Пu states of dimer 7Li2

The comparison between single-point energy scanning （SPES） and geometry optimization （OPT） in determining the equilibrium geometries of c^3∑g^＋ and B^1-Пu states of dimer 7Li2 is made at numerous basis sets by using a symmetryadapted-cluster configuration-interaztion （SAC-CI） method in the Gaussian 03 program package. In this paper the difference of the equilibrium geometries obtained by SPES and by OPT is reported. The results obtained by SPES are found to be more reasonable than those obtained by OPT in full active space at the present SAC-CI level of theory. And the conclusion is attained that the cc-PVTZ is a most suitable basis set for these states. The calculated dissociation energies and equilibrium geometries are 0.8818 eV and 0.3090 nm for c^3∑g^＋ state, and 0.3668 eV and 0.2932 nm for B^1-Пu state respectively. The potential energy curves are calculated over a wide internuclear distance range from about 2.5α0 to 37α0 and have a least-squares fit into the Murrell-Sorbie function. According to the calculated analytic potential energy functions, the harmonic frequencies （We） and other spectroscopic data （ωeXe, Be and αe） are calculated. Comparison of the theoretical determinations at present work with the experiments and other theories clearly shows that the present work is the most complete effort and thus represents an improvement over previous theoretical results.

Analytical Potential Energy Function,Spectroscopic Constants and Vibrational Levels for A^1E_u^+ State of Dimer ~7Li_2

The symmetry-adapted-duster configuration-interaction method is used to investigate the spectroscopicproperties of ~7Li_2(A^1∑_u^+) over the internuclear distance ranging from 2.4ao to 37ao.The complete potential energycurves are calculated at numbers of basis sets.All the ab initio calculated points are fitted to the analytic MurrellSorbie function and then employed to compute the spectroscopic constants.By comparison,the spectroscopic constantsreproduced by the potential attained at D95(3df,3pd) are found to be very close to the experiments,a^d the values (T_e,D_e,R_e,ω_e,ω_eχ_e,α_e and B_e) are of 1.732 93 eV,1.161 36 eV,0.313 27 nm,251.95 cm^(-1),1.623 cm^(-1),0.005 35 cm^(-1),and0.490 cm^(-1),respectively.With the potential obtained at D95(3df,3pd),the totally 75 vibrational states are found whenJ=0.The vibrational levels,the classical turning points and the inertial rotation constants of the first 68 vibrationalstates are calculated for the first time and compared with the available measurements.Good agreement is obtained.The centrifugal distortion constants of the first 32 vibrational states are also reported for the first time.The reasonabledissociation limit for ~7Li_2(A^1∑_u^+) is deduced using the calculated results at present.