Fully flexible unit cell simulation with recursive thermostat chains

The recursive thermostat chained fully flexible cell molecular dynamic simulation (NsigmaT ensemble) is performed. The ensemble is based on the metric tensor, whose components are used as extended variables. These variables are combined with Nosé-Poincaré recursive thermostat chains. This extended Hamiltonian approach preserves Hamiltonian in structure, and the partition function satisfies the NsigmaT ensemble state in phase space. In the present study, the generalized leap frog method was employed for time integration. The resulting molecular dynamics simulation was performed for bulk and thin film solid materials in the face-centered-cubic crystal structure. Uniaxial tension test and simple shear test are performed to predict the behaviors of a solid material in the bulk state and nanoscale thin film state. The proposed flexible cell method should serve as a powerful tool for the prediction of mechanical and thermal properties of solid materials including nanoscale behavior.     

动力学方程控制表面反应的模拟模型和方法

提出了动力学方程控制表面反应的模拟模型和方法.该模型从最基本的质量作用定律出发,获得表面反应的动力学方程.而表面反应通过格子模拟反应器进行.通过表面催化样板反应"CO表面催化氧化"检验了该模拟模型和方法,与实验结果吻合.该模型可在其它复杂的表面催化反应体系中推广应用.     

基于分子间相互作用的纳米尺度分子传递

纳米尺度下的分子传递是以纳米先进材料为导向的材料化学工程学科所面临的关键科学问题之一.借鉴分子热力学的建模研究思路研究分子传递,从分子之间相互作用出发,结合分子模拟技术,有望最终建立理论模型,实现分子传递的定量预测.本文通过几个研究实例初步探索了如何从分子间相互作用出发开展纳米尺度下分子传递的研究,利用分子模拟手段解析纳米尺度下特殊的微结构,并以此为基础进而实现对分子传递行为的调控和预测,指导具有丰富纳米结构的膜材料以及催化材料的设计和应用.     

Real‐Time Monitoring of Mass‐Transport‐Related Enzymatic Reaction Kinetics in a Nanochannel‐Array Reactor

To understand the fundamentals of enzymatic reactions confined in micro‐/nanosystems, the construction of a small enzyme reactor coupled with an integrated real‐time detection system for monitoring the kinetic information is a significant challenge. Nano‐enzyme array reactors were fabricated by covalently linking enzymes to the inner channels of a porous anodic alumina (PAA) membrane. The mechanical stability of this nanodevice enables us to integrate an electrochemical detector for the real‐time monitoring of the formation of the enzyme reaction product by sputtering a thin Pt film on one side of the PAA membrane. Because the enzymatic reaction is confined in a limited nanospace, the mass transport of the substrate would influence the reaction kinetics considerably. Therefore, the oxidation of glucose by dissolved oxygen catalyzed by immobilized glucose oxidase was used as a model to investigate the mass‐transport‐related enzymatic reaction kinetics in confined nanospaces. The activity and stability of the enzyme immobilized in the nanochannels was enhanced. In this nano‐enzyme reactor, the enzymatic reaction was controlled by mass transport if the flux was low. With an increase in the flux (e.g., >50 μL min^?1), the enzymatic reaction kinetics became the rate‐determining step. This change resulted in the decrease in the conversion efficiency of the nano‐enzyme reactor and the apparent Michaelis–Menten constant with an increase in substrate flux. This nanodevice integrated with an electrochemical detector could help to understand the fundamentals of enzymatic reactions confined in nanospaces and provide a platform for the design of highly efficient enzyme reactors. In addition, we believe that such nanodevices will find widespread applications in biosensing, drug screening, and biochemical synthesis.     

Analysis of the slip effect on the permeate flux in membrane ultrafiltration

A method for predicting the mass transfer coefficient as well as the limiting permeate flux in membrane ultrafiltration has been found, based upon the boundary-layer theory which takes into account the slip velocity on the membrane surface. The theory presupposes the existence of a slip flow on a porous membrane surface, especially for the limiting permeate-flux operations. Further, the slip velocity increases with the size of the pores of the membrane, with feed velocity and also with feed concentration. The theory also showed that the permeate flux increases with the increase of the slip velocity. A considerable improvement in theoretical prediction of the permeate flux is expected if the slip flow effect is taken into consideration.     

Computer simulation of reverse micelles and water-in-oil microemulsions

The literature data are reviewed on molecular simulation of reverse micelles and water-in-oil microemulsions by the molecular dynamics and Monte Carlo methods. Different models of reverse micelles from a spherical cavity with an impenetrable wall to an atomistic ensemble of surfactant molecules are considered. The main structural and thermodynamic properties, as well as the dynamics of micelle components are considered. The results are compared with the data obtained using both a single model and models of different levels.     

Flow field in a shrinking-bed reactor for pretreatment of cellulosic biomass

A shrinking-bed reactor was designed by the National Renewable Energy Laboratory to maintain a constant bulk packing density of cellulosic biomass. The high solid-to-liquid ratio in the pretreatment process allows a high sugar yield and avoids the need to flush large volumes of solution through the reactor. The shrinking-bed reactor is a promising pretreatment reactor with the potential for scale-up for commercial applications. To scale up the shrinking-bed reactor, it is necessary to understand the flow pattern in the reactor. In this study, flow field is simulated with computational fluid dynamics using a porous medium model. Different discrete “snapshots” and multiple steady states are utilized. The bulk flow pattern, velocity distribution, and pressure drop are determined from the simulation and can be used to guide reactor design and scale-up.     

Path ensembles and path sampling in nonequilibrium stochastic systems

Markovian models based on the stochastic master equation are often encountered in single molecule dynamics, reaction networks, and nonequilibrium problems in chemistry, physics, and biology. An efficient and convenient method to simulate these systems is the kinetic Monte Carlo algorithm which generates continuous-time stochastic trajectories. We discuss an alternative simulation method based on sampling of stochastic paths. Utilizing known probabilities of stochastic paths, it is possible to apply Metropolis Monte Carlo in path space to generate a desired ensemble of stochastic paths. The method is a generalization of the path sampling idea to stochastic dynamics, and is especially suited for the analysis of rare paths which are not often produced in the standard kinetic Monte Carlo procedure. Two generic examples are presented to illustrate the methodology.     

Collective motion artifacts arising in long‐duration molecular dynamics simulations

We tested a variety of molecular dynamics simulation strategies in long‐duration (up to several nanoseconds) constant‐temperature simulations of liquid water under periodic boundary conditions. Such long durations are necessary to achieve adequate conformational sampling in simulations of membrane assemblies and other large biomolecular systems. Under a variety of circumstances, serious artifacts arise in the form of spurious collective behavior that becomes obvious only after the simulation has gone at least several hundred picoseconds. The potential energy of the system drops and the system changes from a liquid to an icy or glassy state. The underlying cause is accumulated center‐of‐mass motion of the system, coupled with velocity rescaling associated with constant‐temperature control. The velocity rescaling in the constant‐temperature algorithm reduces the thermal velocity as the net center‐of‐mass velocity grows, effectively causing the kinetic energy of the system to drain from thermal motions into coordinated motions. We found that the incidence and magnitude of the underlying artifactual motion leading to the spurious transition is mediated by: choice of method for computing electrostatic interactions; choice of ensemble; size of the simulation cell; SHAKE tolerance; frequency of nonbonded pairlist updating; and closeness of coupling to the temperature bath. The appearance of the spurious transition can be avoided by periodically subtracting net center‐of‐mass motion during the dynamics, or by improving the accuracy of the simulation by means of tightening SHAKE tolerance and updating nonbonded pairlists every timestep. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 121–131, 2000     

Independent trajectory implementation of the semiclassical Liouville method: application to multidimensional reaction dynamics

We describe an independent trajectory implementation of semiclassical Liouville method for simulating quantum processes using classical trajectories. In this approach, a single ensemble of trajectories describes all semiclassical density matrix elements of a coupled electronic state problem, with the ensemble evolving classically under a single reference Hamiltonian chosen on the basis of physical grounds. In this paper, we introduce an additional uncoupled trajectory approximation, allowing the members of the ensemble to evolve independently of one another and eliminating the major computational costs of our previous coupled trajectory implementation. The accuracy of the method is demonstrated for model one-dimensional problems. In addition, the approach is applied to the chemical reaction dynamics of a collinear triatomic system, yielding excellent agreement with exact calculations. This method allows molecular dynamics involving coupled electronic surfaces to be modeled with essentially the same effort as classical molecular dynamics and ensemble averaging.     

Nanophase segregation and water dynamics in the dendrion diblock copolymer formed from the Fréchet polyaryl ethereal dendrimer and linear PTFE

We propose a new material consisting of a dendrion copolymer formed from (a) a water-soluble dendritic polymer and (b) a hydrophobic backbone. Using molecular dynamics simulations techniques, we determine the structure and dynamics of the dendrion formed by second-generation Fréchet polyaryl ethereal dendrimer as the hydrophilic component and linear polytetrafluoroethylene (PTFE) as the hydrophobic polymer, with 5 and 10 wt % of water. We find that this material produces a well-developed nanoscale structure in which water forms a continuous nanophase, making this new family of compounds promising candidates for applications in fuel cell membranes. We find that the water molecules are incorporated into the dendrimer block of the copolymer to form a nanophase-segregated structure. The well-developed nanophase-segregated structures rendered by this material have characteristic dimensions of segregation ( approximately 30 Angstrom) and dendrimer conformational properties that are independent of water content. Calculations of water dynamics and proton transport in these nanophase-segregated structures indicate that the dendrion copolymer membrane with 10 wt % of water content has a water structure and transport properties equivalent to that of the hydrated Nafion membrane with 20 wt % of water content.     

Monte Carlo adiabatic simulation of equilibrium reacting systems: The ammonia synthesis reaction

We present an application of the recently developed Monte Carlo method for simulations at fixed total enthalpy [W. R. Smith, M. Lísal, Phys. Rev. E 66 (2002) 01114-1–01114-3], combined with the reaction ensemble Monte Carlo method, for the direct prediction of equilibrium reactive adiabatic processes. For the industrially important ammonia synthesis reaction in an adiabatic plug-flow reactor, we perform direct simulations of the equilibrium reaction temperature and the composition of the exit stream as a function of the temperature and pressure of the inlet stream. The chemical species of the system are represented by all-atom potentials with interaction parameters taken from the literature. The accuracy of the molecular model is validated by comparing simulation results with experimental data. We also compare the simulation results with a macroscopic thermodynamic model based on the Soave–Redlich–Kwong equation of state. The simulation results for the reaction conversion show very good agreement with available experimental data over a wide range of temperatures and pressures, whereas the corresponding results from the macroscopic thermodynamic model slightly deteriorate with increasing pressure. Based on these comparisons, the predicted values of the reaction temperature and composition of the exit stream from the simulations are more accurate than the corresponding predicted values from the macroscopic thermodynamic model.     

Rotational and spin viscosities of water: Application to nanofluidics

In this paper we evaluate the rotational viscosity and the two spin viscosities for liquid water using equilibrium molecular dynamics. Water is modeled via the flexible SPC/Fw model where the Coulomb interactions are calculated via the Wolf method which enables the long simulation times required. We find that the rotational viscosity is independent of the temperature in the range from 284 to 319 K. The two spin viscosities, on the other hand, decrease with increasing temperature and are found to be two orders of magnitude larger than that estimated by Bonthuis et al. [Phys. Rev. Lett. 103, 144503 (2009)] We apply the results from molecular dynamics simulations to the extended Navier-Stokes equations that include the coupling between intrinsic angular momentum and linear momentum. For a flow driven by an external field the coupling will reduce the flow rate significantly for nanoscale geometries. The coupling also enables conversion of rotational electrical energy into fluid linear momentum and we find that in order to obtain measurable flow rates the electrical field strength must be in the order of 0.1?MV?m(-1) and rotate with a frequency of more than 100 MHz.     

Humectant release from membrane materials

We report the results of membrane filtration studies designed to measure the removal of humectant preservatives (expressed as total organic carbon) from new membrane samples. Membranes with different characteristic properties, that is, relative molecular mass cutoff and material chemistry, were filtered with deionized water under constant flux and feed water temperature (in either dead-end or cross-flow devices) to determine the area-normalized filtrate volume required to remove all of the measurable organic carbon. For specific cases, the effects of changing flux and feed water temperature are also reported. Release of humectants depends on the nominal relative molecular mass cutoff and the thickness (including support) of the membrane—complete removal is not simply predicted by a soaking time or measured volume of deionized water filtered through the membrane without regard to the flux. This report provides general guidance and a suggested measurement technique for monitoring the removal of membrane preservatives prior to membrane application studies.     

Molecular dynamics coupled with a virtual system for effective conformational sampling

An enhanced conformational sampling method is proposed: virtual‐system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free‐energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.     

Simulation of steady-state diffusion: Driving force ensured by dual control volumes or local equilibrium Monte Carlo

We provide a systematic comparative analysis of various simulation methods for studying steady-state diffusive transport of molecular systems. The methods differ in two respects: (1) the actual method with which the dynamics of the system is handled can be a direct simulation technique [molecular dynamics (MD) and dynamic Monte Carlo (DMC)] or can be an indirect transport equation [the Nernst-Planck (NP) equation], while (2) the driving force of the steady-state transport can be maintained with control cells on the two sides of the transport region [dual control volume (DCV) technique] or it can be maintained in the whole simulation domain with the local equilibrium Monte Carlo (LEMC) technique, where the space is divided into small subvolumes, different chemical potentials are assigned to each, and grand canonical Monte Carlo simulations are performed for them separately. The various combinations of the transport-methods with the driving-force methods have advantages and disadvantages. The MD+DCV and DMC+DCV methods are widely used to study membrane transport. The LEMC method has been introduced with the NP+LEMC technique, which was proved to be a fast, but somewhat empirical method to study diffusion [D. Boda and D. Gillespie, J. Chem. Theor. Comput. 8, 824 (2012)]. In this paper, we introduce the DMC+LEMC method and show that the resulting DMC+LEMC technique has the advantage over the DMC+DCV method that it provides better sampling for the flux, while it has the advantage over the NP+LEMC method that it simulates dynamics directly instead of hiding it in an external adjustable parameter, the diffusion coefficient. The information gained from the DMC+LEMC simulation can be used to construct diffusion coefficient profiles for the NP+LEMC calculations, so a simultaneous application of the two methods is advantageous.     

High temperature molecular beam source reactor

Small low residence time flow tube reactors made of alumina and used as molecular beam sources are described. In these reactors, gas mixtures are rapidly heated and brought to reaction. The composition of the gas leaving the reactor is analyzed by molecular beam mass spectroscopy. For quantitative simulation of the reacting gas flow, the theory of one-dimensional compressible flow with friction, heat transfer, and chemical reaction is brought into a form suitable for practical computation. The system has been applied to study the thermal decompositions of O₃ and N₂O. The experimental results on both reactions can be well modeled by homogeneous reaction mechanisms with accepted rate constants. Heterogeneous reaction steps are shown to be unimportant.