A molecular mechanics force field for lignin

A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. Finally, the force field is validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this lignin force field will enable full simulations of lignocellulose.     

Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space

A new method is presented that docks molecular fragments to a rigid protein receptor. It uses a probabilistic procedure based on statistical thermodynamic principles to place ligand atom triplets at the lowest energy sites. The probabilistic method ranks receptor binding modes so that the lowest energy ones are sampled first. This allows constraints to be introduced to limit the depth of the search leading to a computationally efficient method of sampling low energy conformational space. This is combined with energy minimization of the initial fragment placement to arrive at a low energy conformation for the molecular fragment. Two different search methods are tested involving (i) geometric hashing and (ii) pose clustering methods. Ten molecular fragments were docked that have commonly been used to test docking methods. The success rate was 8/10 and 10/10 for generating a close solution ranked first using the two different sampling procedures. In general, all five of the top ranked solutions reproduce the observed binding mode, which increases confidence in the predictions. A set of ten molecular fragments that have previously been identified as problematic were docked. Success was achieved in 3/10 and 4/10 using the two different methods. Again there is a high level of agreement between the two methods and again in the successful cases the top ranked solutions are correct whilst in the case of the failures none are. The geometric hashing and pose clustering methods are fast averaging 13 and 11 s per placement respectively using conservative parameters. The results are very encouraging and will facilitate the process of finding novel small molecule lead compounds by virtual screening of chemical databases.     

Deriving effective mesoscale potentials from atomistic simulations

We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes.     

A NEW CUMULUS PARAMETERIZATION SCHEME AND ITS APPLICATION TO PRECIPITATION NUMERICAL PREDICTION

According to the characteristics of cumulus and stratiform clouds during the meiyu period (plum rains) over Jianghuai valleys (the Changjiang (Yangtze) River and the Huaihe River), a modified Kuo-type cumulus parameterization scheme applicable to midlatitude con-vective systems is suggested in this paper. It is often observed that cumulus and stratiform clouds coexist in a rain-bearing synoptic systems and the precipitation amount associated with this system may be amplified by their interaction. With some important processes of cloud physics taken into account, we use a simple seeder-feeder model (including colloidal instability, collision effect and entrainment) to describe this process of interaction within framework of Kuo-type cumulus parameterization. It is found that the rainfall amount caused by ice crystal effect accounts for 30-40% of total rainfall, but the collision effect is not so great generally. We introduced this scheme to the regional numerical model used by Wuhan Observatory of Hubei     

The zone of flow establishment for plumes with significant buoyancy

The self-similar assumption used in jet and plume models is only valid for distances of greater than about six stack diameters downstream, in the zone of established flow (ZEF). The ‘Gaussian’ profile, observed at the beginning of the ZEF, must be related to source ‘top hat’ parameter values. However, previously used formulae are shown here to be approximations, being valid only for non-buoyant sources (‘pure jets’). Extensions to sources of significant buoyancy are described in terms of the densimetric Froude number, based on recently published experimental work.     

Optimal control computation for linear time-lag systems with linear terminal constraints

A computational scheme using the technique of control parameterization is developed for solving a class of optimal control problems involving linear hereditary systems with bounded control region and linear terminal constraints. Several examples have been solved to illustrate the efficiency of the technique.The authors wish to thank Dr. B. D. Craven for pointing out an error in an earlier version of this paper.From January 1985, Associate Professor, Department of Industrial and Systems Engineering, National University of Singapore, Kent Ridge, Singapore.     

A novel feedback controller design with robust fault isolation ability

This paper proposes a novel feedback controller design scheme which can achieve fault isolation based on the control signal or its embedded signal, i.e., with the self-fault-isolation ability. First of all, according to the well-known Youla parameterization, a controller structure consisting of state and residual joint feedback is developed. Then, the residual feedback gain and observer gain are designed to make the cooperative structured residual feedback signal have fault isolation ability. Some free design parameters in the two gains are further utilized for robust self-fault-isolation. Moreover, the state feedback gain is designed, in the framework of switched system, to realize the self-fault-diagnosis and isolation, based on the control signal directly. The proposed control structure also has the advantage of cooperative fault tolerance. Finally, the simulation of HVAC (Heating, Ventilation and Air Conditioning) system, composed of four rooms in one story building scenario, is carried out to demonstrate the effectiveness and superiority of the proposed feedback controller design approach.     

Partial hessian fitting for determining force constant parameters in molecular mechanics

We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond‐stretching, angle‐bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least‐squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER‐type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM‐calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal‐organic frameworks, the MM‐optimized geometry sometimes deviates significantly from the QM‐optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond‐stretching and angle‐bending terms. © 2016 Wiley Periodicals, Inc.     

The Generalized Parameterization Procedure for Semiempirical MO Method and Calculation of ionization Potentials for the Fourth-Period Element Molecules

This study presents a set of the generalized parameters from a unique resource for the elements which are from the first-period to the fourth-period (H to Xe). In addition, these series of parameters are used to examine forty-five compounds consisting of the fourth-period elements and the second-period transition metal elements. Herein, the major calculation theory applied is the s-p-d INDO MO method. To verify the reliability of the molecular calculations, similar calculations of the STO-3G and STO-3G* ab inito methods, along with the semiempirical PM3 and AM1 methods are also compared. Results in this study demonstrate that the s-p-d INDO MO computed with the generalized parameter is the best available method.     

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.