scholarly journals A Force Field for Poly(oxymethylene) Dimethyl Ethers (OMEn)

2021 ◽  
Author(s):  
Aditya Kulkarni ◽  
Edder J. García ◽  
Angelo Damone ◽  
Michael Schappals ◽  
Simon Stephan ◽  
...  
Keyword(s):  
Experimental Data ◽  
Force Field ◽  
Shear Viscosity ◽  
Degrees Of Freedom ◽  
Molecular Geometry ◽  
Pure Liquid ◽  
Critical Properties ◽  
Synthetic Fuels ◽  
Simulation Data ◽  
Internal Degrees Of Freedom

A united atom force field for the homologous series of the poly(oxymethylene)dimethyl ethers (OMEn): H3C–O–(CH2O)n–CH3, is presented. OMEn are oxygenatesand promising new synthetic fuels and solvents. The molecular geometry of the OMEn,the internal degrees of freedom and their electrostatic properties were obtained fromquantum mechanical calculations. To model repulsion and dispersion, Lennard-Jonesparameters were fitted to the experimental liquid densities and vapour pressures of pureOMEn (n “ 1 - 4). The critical properties of OMEn (n “ 1 - 4) were determined fromthe simulation data. Additionally, the shear viscosity of pure liquid OMEn is evaluatedand compared with literature data. Finally, the solubility of CO2 in OME2, OME3and OME4 is predicted using a literature model for CO2 and the Lorentz-Berthelotcombining rules. The results agree well with experimental data from the literature.

scholarly journals Common Force Field Thermodynamics of Cholesterol

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Francesco Giangreco ◽  
Eiji Yamamoto ◽  
Yoshinori Hirano ◽  
Milan Hodoscek ◽  
Volker Knecht ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Force Field ◽  
Dynamic Characteristics ◽  
Degrees Of Freedom ◽  
Force Fields ◽  
Principal Component ◽  
Component Analysis ◽  
Field Independence ◽  
Internal Degrees Of Freedom

Four different force fields are examined for dynamic characteristics using cholesterol as a case study. The extent to which various types of internal degrees of freedom become thermodynamically relevant is evaluated by means of principal component analysis. More complex degrees of freedom (angle bending, dihedral rotations) show a trend towards force field independence. Moreover, charge assignments for membrane-embedded compounds are revealed to be critical with significant impact on biological reasoning.

Driving Torsion Scans with Wavefront Propagation

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Chaya Stern ◽  
mudong feng ◽  
Lee-Ping Wang
Keyword(s):  
Potential Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Initial Guess ◽  
Field Development ◽  
Force Field Development ◽  
Wavefront Propagation ◽  
Open Source Software Package

<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

Force field for in-plane vibrations of terephthalonitrile

1989 ◽  
Vol 54 (1) ◽  
pp. 18-27 ◽  
Author(s):  
Juan F. Arenas ◽  
Juan I. Marcos ◽  
Francisco J. Ramírez
Keyword(s):  
Experimental Data ◽  
Force Field ◽  
Normal Coordinates ◽  
Internal Coordinates ◽  
Isotopic Shifts ◽  
Quadratic Force Field ◽  
Semi Empirical

The general quadratic force field for the in-plane vibrations of terephthalonitrile was calculated by the semi-empirical MINDO/3 method. This force field was refined to the frequencies observed experimentally for terephthalonitrile and isotopic shifts of terephthalonitrile-[15N2]. The refined frequencies reproduce the experimental data with errors less than 0.5%. The normal coordinates and the force field in internal coordinates were also calculated from the refined field.

scholarly journals A novel class of translationally invariant spin chains with long-range interactions

2020 ◽  
Vol 2020 (8) ◽  
Author(s):  
B. Basu-Mallick ◽  
F. Finkel ◽  
A. González-López
Keyword(s):  
Long Range ◽  
Degrees Of Freedom ◽  
Spin Chains ◽  
Open Chain ◽  
New Class ◽  
Spin Interactions ◽  
Long Range Interactions ◽  
Spin Reversal ◽  
Twisted Yangian ◽  
Internal Degrees Of Freedom

Abstract We introduce a new class of open, translationally invariant spin chains with long-range interactions depending on both spin permutation and (polarized) spin reversal operators, which includes the Haldane-Shastry chain as a particular degenerate case. The new class is characterized by the fact that the Hamiltonian is invariant under “twisted” translations, combining an ordinary translation with a spin flip at one end of the chain. It includes a remarkable model with elliptic spin-spin interactions, smoothly interpolating between the XXX Heisenberg model with anti-periodic boundary conditions and a new open chain with sites uniformly spaced on a half-circle and interactions inversely proportional to the square of the distance between the spins. We are able to compute in closed form the partition function of the latter chain, thereby obtaining a complete description of its spectrum in terms of a pair of independent su(1|1) and su(m/2) motifs when the number m of internal degrees of freedom is even. This implies that the even m model is invariant under the direct sum of the Yangians Y (gl(1|1)) and Y (gl(0|m/2)). We also analyze several statistical properties of the new chain’s spectrum. In particular, we show that it is highly degenerate, which strongly suggests the existence of an underlying (twisted) Yangian symmetry also for odd m.

scholarly journals Dissipative dynamics of a particle coupled to a field via internal degrees of freedom

2021 ◽  
Vol 103 (5) ◽  
Author(s):  
Kanupriya Sinha ◽  
Adrián Ezequiel Rubio López ◽  
Yiğit Subaşı
Keyword(s):  
Degrees Of Freedom ◽  
Dissipative Dynamics ◽  
Internal Degrees Of Freedom

scholarly journals Optimal Relabeling of Water Molecules and Single-Molecule Entropy Estimation

Biophysica ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 279-296
Author(s):  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Single Molecule ◽  
Degrees Of Freedom ◽  
Water Molecules ◽  
Maximum Information ◽  
Nearest Neighbours ◽  
Biomolecular Simulations ◽  
Solvent Molecules ◽  
Solvation Entropy ◽  
Dynamics Simulations ◽  
Internal Degrees Of Freedom

Estimation of solvent entropy from equilibrium molecular dynamics simulations is a long-standing problem in statistical mechanics. In recent years, methods that estimate entropy using k-th nearest neighbours (kNN) have been applied to internal degrees of freedom in biomolecular simulations, and for the rigorous computation of positional-orientational entropy of one and two molecules. The mutual information expansion (MIE) and the maximum information spanning tree (MIST) methods were proposed and used to deal with a large number of non-independent degrees of freedom, providing estimates or bounds on the global entropy, thus complementing the kNN method. The application of the combination of such methods to solvent molecules appears problematic because of the indistinguishability of molecules and of their symmetric parts. All indistiguishable molecules span the same global conformational volume, making application of MIE and MIST methods difficult. Here, we address the problem of indistinguishability by relabeling water molecules in such a way that each water molecule spans only a local region throughout the simulation. Then, we work out approximations and show how to compute the single-molecule entropy for the system of relabeled molecules. The results suggest that relabeling water molecules is promising for computation of solvation entropy.

Three-dimensional asymmetric maximum weight lifting prediction considering dynamic joint strength

2021 ◽  
pp. 095441192098703
Author(s):  
Rahid Zaman ◽  
Yujiang Xiang ◽  
Jazmin Cruz ◽  
James Yang
Keyword(s):  
Experimental Data ◽  
Degrees Of Freedom ◽  
Inverse Dynamics ◽  
Three Dimensional ◽  
Optimization Method ◽  
Weight Lifting ◽  
Joint Torque ◽  
Maximum Weight ◽  
Angular Velocities ◽  
Asymmetric Lifting

In this study, the three-dimensional (3D) asymmetric maximum weight lifting is predicted using an inverse-dynamics-based optimization method considering dynamic joint torque limits. The dynamic joint torque limits are functions of joint angles and angular velocities, and imposed on the hip, knee, ankle, wrist, elbow, shoulder, and lumbar spine joints. The 3D model has 40 degrees of freedom (DOFs) including 34 physical revolute joints and 6 global joints. A multi-objective optimization (MOO) problem is solved by simultaneously maximizing box weight and minimizing the sum of joint torque squares. A total of 12 male subjects were recruited to conduct maximum weight box lifting using squat-lifting strategy. Finally, the predicted lifting motion, ground reaction forces, and maximum lifting weight are validated with the experimental data. The prediction results agree well with the experimental data and the model’s predictive capability is demonstrated. This is the first study that uses MOO to predict maximum lifting weight and 3D asymmetric lifting motion while considering dynamic joint torque limits. The proposed method has the potential to prevent individuals’ risk of injury for lifting.

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