GPU accelerated implementation of NCI calculations using promolecular density

The NCI approach is a modern tool to reveal chemical noncovalent interactions. It is particularly attractive to describe ligand–protein binding. A custom implementation for NCI using promolecular density is presented. It is designed to leverage the computational power of NVIDIA graphics processing unit (GPU) accelerators through the CUDA programming model. The code performances of three versions are examined on a test set of 144 systems. NCI calculations are particularly well suited to the GPU architecture, which reduces drastically the computational time. On a single compute node, the dual‐GPU version leads to a 39‐fold improvement for the biggest instance compared to the optimal OpenMP parallel run (C code, icc compiler) with 16 CPU cores. Energy consumption measurements carried out on both CPU and GPU NCI tests show that the GPU approach provides substantial energy savings. © 2017 Wiley Periodicals, Inc.     

A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent–solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed‐ups up to a factor of 54 (single‐precision GPU vs. double‐precision CPU) could be achieved. The accuracy of the single‐precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent–solvent interaction evaluation on a GPU, and thus, to speed‐up their simulations by a factor 6–9. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Three-dimensional numerical simulation of viscoelastic phase separation under shear: the roles of bulk and shear relaxation moduli

The morphological, dynamic and rheological characteristics in the viscoelastic phase separation(VPS) of sheared polymer solutions are investigated by three-dimensional(3D) numerical simulations of viscoelastic model. The simulations are accelerated by graphic process unit(GPU) to break through the limitation of computation power. Firstly, the morphological and dynamic characteristics of VPS under shear are presented by comparing with those in classic phase separation(CPS). The results show that the phase inversion and phase shrink take place in VPS under shear. Then, the roles of bulk and shear relaxation moduli in VPS are investigated in details. The bulk relaxation modulus slows down the phase separation process under shear, but not affects the dynamic path of VPS. The dynamic path can be divided into three stages: freezing stage, growth stage and stable stage. The second overshoot phenomenon in the shear stress is observed, and explained by the breakdown and reform of string structures. The shear modulus affects morphology evolution in the late stage of VPS under shear.     

Further study of the viscoelastic phase separation of cyanate ester modified with poly(ether imide)

In this study, the viscoelastic phase separation process was studied further by time‐resolved light scattering, differential scanning calorimetry, and scanning electron microscopy in the system of poly(ether imide)‐modified bisphenol‐A dicyanate. It was observed that the evolution time of phase structure and relaxation time of diffusion flow of the bisphenol‐A dicyanate were similar with the phase diagram of curing conversion versus content of PEI. The results suggested that the viscoelastic phase separation was affected by the curing conversion of the system at the onset point of phase separation. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 517–523, 2006     

Monte Carlo simulation of phase separation kinetics in a concentrated polymer solution

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Polymerization-induced phase separation in polyether-sulfone modified epoxy resin systems: effect of curing reaction mechanism

Polyethersulfone (PES)-modified epoxy systems with stepwise reaction were studied throughout the entire curing process by using optical microscopes, time-resolved light scattering (TRLS), and a rheolometry instrument compared with that of chainwise polymerization. The results suggested that the phase separation process is mainly controlled by the diffusion of epoxy oligomers for stepwise mechanism system and by that of epoxy monomers for chainwise mechanism system. In case of high PES content (SPES-20%) light-scattering results showed a viscoelastic phase separation and the characteristic relaxation time of phase separation can be described well by the WLF equation. However, in the case of low PES content (SPES-14%) secondary phase separation phenomenon was observed by Optical Microscope and further demonstrated by rheological study.     

Chain conformations and phase separation in polymer solutions with varying solvent quality

Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the polymer-solvent interaction strength is increased further to be more than about twice the strength of the polymer-polymer and solvent-solvent interactions, the chain exhibits an unexpected collapsing behavior. Correspondingly, for strong polymer-solvent attractions, phase separation is observed in the solutions of multiple chains. These results indicate that the solvent becomes effectively poor again at very attractive polymer-solvent interactions. Nonetheless, the mechanism of chain collapsing and phase separation in this limit differs from the case with a poor solvent rendered by unfavorable polymer-solvent interactions. In the latter, the solvent is excluded from the domain of the collapsed chains while in the former, the solvent is still present in the pervaded volume of a collapsed chain or in the polymer-rich domain that phase separates from the pure solvent. In the limit of strong polymer-solvent attractions, the solvent behaves as a glue to stick monomers together, causing a single chain to collapse and multiple chains to aggregate and phase separate.     

Studies on phase separation and coarsening in blends of poly(vinylidene-fluoride) and poly(ethyl-acrylate)

The phase diagram of blends of poly(vinylidene fluoride) and poly (ethyl acrylate) was established by X-ray scattering, optical microscopy and calorimetric techniques. Structure formation, involving phase separation and coarsening was analyzed as a function of temperature variations and annealing times. The variations consisted of increasing or decreasing the temperature stepwise, starting either in the one-phase or in the two-phase state of the melt.Dedicated to Prof. R. Bonart (Univ. Regensburg) on the occasion of his 60^th birthday     

Kinetics of phase separation in polymer blends. Calculations based on nonlinear theory

Suzuki's scaling theory for transient phenomena is applied to the calculation of the kinetics of phase separation in the early-to-intermediate stage based on a nonlinear theory proposed by Langer, Bar-on, and Miller (LBM). Calculated results are compared with experimental data on light scattering from a polymer blend system. Deviations from predictions of Cahn's linearized theory in the early time range of phase separation can be explained well by the proposed method of calculation. Nonlinear effects are found to play an essential role in characterizing the light scattering behavior of phase separation in the intermediate stage. Time evolutions of the single-point distribution function of composition are calculated, and the results are in good agreement with those reported in digital imaging analysis experiments and computer simulations of the time-dependent Ginzburg-Landau equation. The influence of asymmetry of free-energy on the single-point distribution function is also investigated in this study. © 1993 John Wiley & Sons, Inc.     

Phase separation by continuous quenching: similarities between cooling experiments in polymer blends and reaction-induced phase separation in modified thermosets

Small angle light scattering (SALS) has been applied to study the phase separation kinetics in a binary polymer mixture of poly(ethyl methyl siloxane) (PEMS) and poly(dimethyl siloxane) (PDMS). The phase separation was induced by cooling an initially homogeneous mixture with well defined cooling rates. The results have been compared to time resolved SALS and microscopy in the course of reaction-induced phase separation in mixtures of an epoxy resin and polysulfone (PSU). For the critical PEMS/PDMS mixture with an upper critical point it was found in a continuous quenching experiment that the time evolution of the scattered light intensity I(q,t) scales with the cooling rate. The similarity to the scaling behavior of I(q,t) in isothermal experiments after fast quenches (scaled by the quench depth) is discussed. A secondary phase separation was found and has been explained by the competition between the growth of the two phase structure during cooling and the mutual diffusion without the assumption of gelation or vitrification. For the epoxy/PSU mixture with 15% PSU, after the appearance of a bicontinuous structure a secondary phase separation was observed. Mixtures with higher PSU-contents formed epoxy-rich droplets in the PSU-rich matrix by nucleation and growth mechanism. The frustration of the structure growth can be explained by approaching vitrification of one or both phases. The similarity between continuous cooling experiments in blends and the reaction-induced phase separation have been discussed in the generalized χN vs. composition phase diagram (N: degree of polymerization, χ: Flory-Huggms interaction parameter).     

Synthesis of thermally-induced phase separating polymer with well-defined polymer structure by living cationic polymerization. I. Synthesis of poly(vinyl ether)s with oxyethylene units in the pendant and its phase separation behavior in aqueous solution

Living cationic polymerization of alkoxyethyl vinyl ether [CH₂?CHOCH₂CH₂OR; R: CH₃ (MOVE), C₂H₅ (EOVE)] and related vinyl ethers with oxyethylene units in the pendant was achieved by 1-(isobutoxy)ethyl acetate ( 1 )/Et_1.5AlCl_1.5 initiating system in the presence of an added base (ethyl acetate or THF) in toluene at 0°C. The polymers had a very narrow molecular weight distribution (M?_w/M?_n = 1.1–1.2) and the M?_n proportionally increased with the progress of the polymerization reaction. On the other hand, the polymerization by 1 /EtAlCl₂ initiating system in the presence of ethyl acetate, which produces living polymer of isobutyl vinyl ether, yielded the nonliving polymer. When an aqueous solution of the polymers thus obtained was heated, the phase separation phenomenon was clearly observed in each polymer at a definite critical temperature (T_ps). For example, T_ps was 70°C for poly(MOVE), and 20°C for poly(EOVE) (1 wt % aqueous solution, M?_n ～ 2 × 10⁴). The phase separation for each case was quite sensitive (ΔT_ps = 0.3–0.5°C) and reversible on heating and cooling. The T_ps or ΔT_ps was clearly dependent not only on the structure of polymer side chains (oxyethylene chain length and ω-alkyl group), but also on the molecular weight (M?_n = 5 × 10³-7 × 10⁴) and its distribution. © 1992 John Wiley & Sons, Inc.     

Numerical simulation of three‐dimensional polymer extrusion flow with differential viscoelastic model

The numerical simulation of viscoelastic flow problems is nowadays an effective way of investigating the complex flow mechanism related to practical engineering problems, such as plastic injection, blow molding and extrusion. The mathematical model of a three‐dimensional (3D) viscoelastic flow in a typical contraction die for polymer extrusion is established and a stable solving method is investigated. The penalty finite element method (FEM) is performed to simulate the viscoelastic melts flow in the channel with a differential constitutive model. The discrete elastic‐viscous split stress (DEVSS) formulation and the streamline‐upwind Petrov–Galerkin (SUPG) technology are employed to improve the computation stability. Both the implementation of the numerical scheme and its application in the practical process analysis are investigated. The effects of various calculation control parameters and different material parameters upon the numerical results are discussed. The 3D flow patterns in the extrusion die with different contraction angles are further investigated based on the above discussions. Copyright © 2007 John Wiley & Sons, Ltd.     

制备方法对聚合物共混物相分离与黏弹弛豫的影响

采用小角激光光散射(SALLS)和动态流变方法研究了通过不同制备方法得到的等规聚丙烯/乙丙橡胶共混物(iPP/EPR)的相分离行为与黏弹行为.依据Cahn-Hilliard-Cook理论分析了熔融共混和溶液共混法制备的质量比为60/40和40/60的iPP/EPR共混物在恒温相分离早期的动力学,发现熔融共混iPP/EPR具有更大的表观扩散系数(Dapp).相分离中后期的实验结果表明,当相区尺寸增长程度相同时,熔融共混试样所用时间更短.表明熔融共混iPP/EPR试样具有更快的相分离速率.动态流变测试结果表明,与溶液共混相比,熔融共混试样具有更快的松弛速率.考虑到相分离过程实质是由高分子链的运动与扩散所控制,两种方法制备的iPP/EPR共混物相分离速率的差异应归于其分子链运动能力的不同.     

On the nature of phase separation of polymer solutions at high extension rates

Experiments with stretching moderately concentrated polymer solutions have been carried out. Model experiments were carried out for poly(acrylonitrile) solutions in dimethyl siloxane. Just the choice of concentrated solutions allowed for a clear demonstration of a demixing effect with the formation of two separate phases—an oriented polymer fiber and solvent drops sitting on its surface. An original experimental device for following all subsequent stages in the demixing process was built. It combined two light beams, one transverse to the fiber and a second directed along (inside) the fiber, the latter played the role of an optical line. This gives a unique opportunity to observe processes occurring inside a fiber. The process of demixing starts from the volume phase separation across the whole cross section of a fiber at some critical deformation and the propagation of the front of demixing along the fiber. Then a solvent cylindrical skin appears which transforms into a system of separate droplets. New experimental data are discussed based on a comparison of the current different points of view on the phenomenon of deformation‐induced phase separation: thermodynamic shift of the equilibrium phase transition temperature, growth of stress‐induced concentration fluctuations in two‐component fluids, and mechanically pressing a solvent out from a polymer network. The general belief is that a rather specific (so‐called “beads‐on‐a‐string”) structure of a filament is realized in stretching dilute solutions: beads of a polymer solution connected by oriented polymer bridges forming a single object. The situation in stretching moderately concentrated solutions appears quite different: real phase separation was observed. So, the alternative phenomenon to the formation of the “beads‐on‐a‐string” structure has been experimentally proven. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 559–565     

Aqueous biphasic systems formed by nonionic polymers II. Concentration effects of inorganic salts on phase separation

Concentration effects of KSCN, KClO₄, KI, KBr, KNO₃, KCl, KF and K₂SO₄ on the compatibility of dextran with ficoll, polyvinylpyrrolidone and poly(ethylene glycol) at fixed polymer concentration ratios were studied in aqueous solution. The results obtained are considered in terms of the Patterson theory of-effect. It is assumed that phase separation in an aqueous solution of two nonionic polymers results from the appearance of two different water structures in the vicinity of the phase polymers. The data obtained are considered in terms of the concept of salting-in-salting-out effects of neutral salts on aqueous solubility of biopolymers. The salt effects observed are attributed to two antagonistic influences of salts on the electrostatic (dipole-dipole) polymer-water interactions and on the water-water interactions in the vicinity of the phase polymers.     

Evidence of mechanisms occurring in thermally induced phase separation of polymeric systems

Thermally induced phase separation is a fabrication technique for porous polymeric structures. By means of easy‐to‐tune processing parameters, such as system composition and demixing temperature, a vast latitude of average pore dimensions, pore size distributions, and morphologies can be obtained. The relation between demixing temperature and morphology was demonstrated via cloud point curve measurement and foams fabrication with controlled thermal protocols, for the model system poly‐l ‐lactide–dioxane–water. The morphologies obtained at a temperature lower than cloud point showed a closed‐pore architecture, suggesting a “nucleation‐and‐growth” separation mechanism, which produced larger pores at higher holding times. Conversely, the porous structures attained when holding the sample above the cloud point exhibited open pores with dimensions independent of time, denoting a phase separation occurring during sample freezing. Finally, the influence of the cooling rate on final morphology was investigated, showing a clear correlation with microstructure and pore size. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 979–983     

Hierarchical porous polymer beads prepared by polymerization-induced phase separation and emulsion-template in a microfluidic device

Porous polymer beads（PPBs） containing hierarchical bimodal pore structure with gigapores and meso-macropores were prepared by polymerization-induced phase separation（PIPS） and emulsion-template technique in a glass capillary microfluidic device（GCMD）. Fabrication procedure involved the preparation of water-in-oil emulsion by emulsifying aqueous solution into the monomer solution that contains porogen. The emulsion was added into the GCMD to fabricate the（water-in-oil）-in-water double emulsion droplets. The flow rate of the carrier continuous phase strongly influenced the formation mechanism and size of droplets. Formation mechanism transformed from dripping to jetting and size of droplets decreased from 550 μm to 250 μm with the increase in flow rate of the carrier continuous phase. The prepared droplets were initiated for polymerization by on-line UV-irradiation to form PPBs. The meso-macropores in these beads were generated by PIPS because of the presence of porogen and gigapores obtained from the emulsion-template. The pore morphology and pore size distribution of the PPBs were investigated extensively by scanning electron microscopy and mercury intrusion porosimetry（MIP）. New pore morphology was formed at the edge of the beads different from traditional theory because of different osmolarities between the water phase of the emulsion and the carrier continuous phase. The morphology and proportion of bimodal pore structure can be tuned by changing the kind and amount of porogen.     

Kinetics of thermally induced phase separation in ternary polymer solutions. I. Modeling of phase separation dynamics

Simulations based on Cahn–Hilliard spinodal decomposition theory for phase separation in thermally quenched polymer/solvent/nonsolvent systems are presented. Two common membrane‐forming systems are studied, cellulose acetate [CA]/acetone/water, and poly(ethersulfone) [PES]/dimethylsulfoxide [DMSO]/water. The effects of initial polymer and nonsolvent composition on the structure‐formation dynamics are elucidated, and growth rates at specific points within the ternary phase diagram are quantified. Predicted pore growth rate curves exhibit a relative maximum with nonsolvent composition. For shallow quenches (lower nonsolvent content) near a phase boundary, the pore growth rate increases with increasing quench depth, whereas for deep quenches, where the composition of the polymer‐rich phase approaches that of a glass, the pore growth rate decreases with increasing quench depth. With increasing initial polymer concentration, the overall rate of structure growth is lowered and the growth rate maximum shifts to higher nonsolvent compositions. This behavior appears to be a universal phenomenon in quenched polymer solutions which can undergo a glass transition, and is a result of an interplay between thermodynamic and kinetic driving forces. These results suggest a mechanism for the locking‐in of the two‐phase structure that occurs during nonsolvent‐induced phase inversion. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1449–1460, 1999     

Measuring the extent of phase separation during polymerization of composite latex particles using modulated temperature DSC

The morphological features of composite latex particles predominantly develop during the polymerization process and depend upon a significant number of variables. In this study, we have concentrated on the relative polarities of the two polymers in the particles and the rate at which we added the monomers during semibatch reactions containing the seed polymer latex. Our particular interest was to develop data that could reveal the extent of polymer phase separation as a function of the amount of monomer fed, and to characterize the morphology resulting from it. While TEM is the most common analytical technique employed, we show in this paper that modulated temperature DSC can generate data that allows us to follow the phase separation process as the monomer feed progresses. By considering the possibilities of having “phases” within the particles of pure polymer, homogeneously mixed (but nonequilibrium) polymers, gradient and interfacial polymer, we have been able to quite successfully simulate the DSC data. This results in quantitative estimates of the relative amounts of these “phases” and their polymer compositions. Combining these results with TEM photos showing the spatial characteristics of the morphology, we can achieve a much greater understanding of the physical structure of the composite latex particles. In many cases we find that phase separation is far from complete at the end of the reaction process. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2790–2806, 2005