Glass transition temperature ($T_{text{g}}$) plays an important role in controlling the mechanical and thermal properties of a polymer. Polyimides are an important category of polymers with wide applications because of their superior heat resistance and mechanical strength. The capability of predicting $T_{text{g}}$ for a polyimide $a~priori$ is therefore highly desirable in order to expedite the design and discovery of new polyimide polymers with targeted properties and applications. Here we explore three different approaches to either compute $T_{text{g}}$ for a polyimide via all-atom molecular dynamics (MD) simulations or predict $T_{text{g}}$ via a mathematical model generated by using machine-learning algorithms to analyze existing data collected from literature. Our simulations reveal that $T_{text{g}}$ can be determined from examining the diffusion coefficient of simple gas molecules in a polyimide as a function of temperature and the results are comparable to those derived from data on polymer density versus temperature and actually closer to the available experimental data. Furthermore, the predictive model of $T_{text{g}}$ derived with machine-learning algorithms can be used to estimate $T_{text{g}}$ successfully within an uncertainty of about 20 degrees, even for polyimides yet to be synthesized experimentally.
When the cooling rate $v$ is smaller than a certain material-dependent threshold, the glass transition temperature $T_g$ becomes to a certain degree the material parameter being nearly independent on the cooling rate. The common method to determine $T_g$ is to extrapolate viscosity $ u$ of the liquid state at temperatures not far above the freezing conditions to lower temperatures where liquid freezes and viscosity is hardly measurable. It is generally accepted that the glass transition occurs when viscosity drops by $13leq nleq17$ orders of magnitude. The accuracy of $T_g$ depends on the extrapolation quality. We propose here an algorithm for a unique determining of $T_g$. The idea is to unambiguously extrapolate $ u(T)$ to low temperatures without relying upon a specific model. It can be done using the numerical analytical continuation of $ u(T)$-function from above $T_g$ where it is measurable, to $Tgtrsim T_g$. For numerical analytical continuation, we use the Pade approximant method.
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further speedup the computations.
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its efficiency, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. In this publication we develop a general method to evaluate the efficiency of these algorithms, which is mostly independent of the parameters of the simulation, and test it for a number of linked cell list algorithms. We also propose a combination of linked cell reordering and interaction sorting that shows a good efficiency for a broad range of simulation setups.
Halogen bonding has emerged as an important noncovalent interaction in a myriad of applications, including drug design, supramolecular assembly, and catalysis. Current understanding of the halogen bond is informed by electronic structure calculations on isolated molecules and/or crystal structures that are not readily transferable to liquids and disordered phases. To address this issue, we present a first-principles simulation-based approach for quantifying halogen bonds in molecular systems rooted in an understanding of nuclei-nuclei and electron-nuclei spatial correlations. We then demonstrate how this approach can be used to quantify the structure and dynamics of halogen bonds in condensed phases, using solid and liquid molecular chlorine as prototypical examples with high concentrations of halogen bonds. We close with a discussion of how the knowledge generated by our first-principles approach may inform the development of classical empirical models, with a consistent representation of halogen bonding.
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems - a one dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb & Dunweg, show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.
Chengyuan Wen
,Binghan Liu
,Josh Wolfgang
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(2020)
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"Determination of Glass Transition Temperature of Polyimides from Atomistic Molecular Dynamics Simulations and Machine-Learning Algorithms"
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Shengfeng Cheng
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