Parallel implementation of isothermal and isoenergetic Dissipative Particle Dynamics using Shardlow-like splitting algorithms

A parallel implementation of the Shardlow splitting algorithm (SSA) for Dissipative Particle Dynamics (DPD) simulations is presented. The isothermal and isoenergetic SSA implementations are compared to the DPD version of the velocity-Verlet integrator in terms of numerical stability and performance. The integrator stability is assessed by monitoring temperature, pressure and total energy for both the standard and ideal DPD fluid models. The SSA requires special consideration due to its recursive nature resulting in more inter-processor communication as compared to traditional DPD integrators. Nevertheless, this work demonstrates that the SSA exhibits stability over longer time steps that justify its regular use in parallel, multi-core applications. For the computer architecture used in this study, a factor of 10–100 speedup is achieved in the overall time-to-solution for isoenergetic DPD simulations and a 15–34 speedup is achieved for the isothermal DPD simulations.     

Numerical and experimental LDL transport through arterial wall

Atherosclerosis develops from oxidized low-density lipoprotein molecules (LDL). When oxidized LDL evolves in plaque formations within an artery wall, a series of reactions occur to repair the damage to the artery wall caused by oxidized LDL. Aim of this study was to compare experimental data of LDL transport through isolated blood vessel with computational results of bounding of oxidized LDL receptor-1 (LOX-1) for endothelial cells with numerical discrete methods such as dissipative particle dynamics (DPD) and lattice Boltzmann (LB) method. Experiments of LDL transport were performed on the isolated rabbit common carotid arteries acquired from fifteen rabbits after 12 weeks of high-fat diet. Oxidative LDL molecule is built and used for docking with LOX-1 receptor. Energies that give the best binding are computed, and the energy with greatest probability of attachment for oxidative LDL molecule and glutamine acid is further used in numerical simulations. Simulations using DPD and LB method use the computed binding energy to calculate the force necessary for binding of LDL molecule to the endothelial blood vessel layer. Experimental results have shown large uptake for shear stress below 1 dyn/cm². Computational results for both discrete methods DPD and LB have shown good accuracy with experimental data. Calculation of the interactive molecule forces from computational chemistry open a new avenue for multiscale modeling methods, which will give better insight for the understanding and the prediction of LDL transport through the arterial wall for the medical community.     

Dissipative particle dynamics simulation of field-dependent DNA mobility in nanoslits

The dynamics of DNA molecules in highly confined nanoslits under varying electric fields are studied using dissipative particle dynamics method, and our results show that manipulation of the electrical field can strongly influence DNA mobility. The mobility of DNA μ scales with electric field E as $ \mu = \mu^{\text{H}} - k_{1} e^{{ - E/E_{c} }} . $ And the data points for different DNA lengths finally approach each other in strong fields, which suggest that the sensitivity to chain length is almost lost. To explain the unusual field-dependent phenomena, we analyze the time evolution of DNA configurations under different fields. For strong driving potentials when the system is dominated by the electric driving force, the DNA chains are more likely to hold coiled configurations. For weak driving potential when the random diffusion forces dominate, we see frequent dynamic transitions between stretched and coiled configuration, which may increase the drag resistance, therefore reduce the mobility.     

Parametric study of fluid–solid interaction for single-particle dissipative particle dynamics model

In this paper, a parametric study of fluid–solid interaction for single-particle dissipative particle dynamics (DPD) model is conducted to describe the hydrodynamic interactions in a large range of particle sizes. To successfully reproduce the hydrodynamics for different particle sizes, and overcome the problem that effective radius of solid sphere does not match its real radius, the cut-off radius and conservative force coefficient of single-particle DPD model have been modified. The cut-off radius and conservative force coefficient are related to the drag force and radial distribution function, so that, for each particle size, they can be determined by DPD simulations. Through numerical fitting, two empirical formulas as a function of spherical radius are developed to calculate the cut-off radius and conservative force coefficient. Numerical results indicate that the single-particle DPD model is, indeed, capable of capturing low Reynolds number hydrodynamic interactions for different particle sizes by selecting these model parameters reasonably. Specifically, the model can not only insure that drag force and torque are quantitatively consistent with theoretical results, but also guarantee the effective radius matches well its real radius. In addition, the shear dissipative force is the major part of drag force and should not be ignored. This study will help to improve the application range of single-particle DPD model to make it suitable for different particle sizes and provide parameter guidance for studying fluid–solid interaction using single-particle DPD model.     

两亲性肽纳米纤维聚集的耗散粒子动力学模拟

根据PA分子基团的化学性质和粒子大小,将PA分子分成DPD粒子,将适当大小的水簇视为溶剂粒子,克服了模拟技巧的困难,首次用耗散粒子动力学(dissipative particle dynamics,DPD)方法模拟了两亲性肽分子PA的自组装相行为.模拟结果表明:在水溶剂的辅助下,在三维纤维状的圆柱聚合体中,这些分子能进行自组装.DPD的模拟结果受溶剂珠粒的大小、温度及PA与溶剂的比例等多种因素的影响.研究同时发现,在圆筒状纤维中,使用5～9个水簇的溶剂粒子可得到PA分子的聚合体.形成纳米纤维聚合体的条件是PA与水珠粒的比值大于1∶6,温度高于340 K.筒状聚合体直径的估计值符合实验测量值.     

Dissipative particle dynamics simulations of liquid nanojet breakup

In this work, we use a dissipative-particle-dynamics (DPD)-based two-phase model to study the breakup of liquid nanojets. We show that the breakup of nanojets is accelerated by the presence of thermal fluctuations. Satellite drops, which are undesirable from an application viewpoint, are not observed in our simulations. We find that the presence of a repulsive wall enclosing the DPD liquid is necessary to prevent clogging of nanojets. We are able to recover the time evolution of minimum jet radius as given by prior theoretical analysis. This study shows that DPD is able to capture the thermal induced breakup phenomena at the sub-micron level. The coarse-grained nature of DPD along with its flexibility to allow for the modeling of complex fluids in combination with the results from this study show that DPD is a useful tool for sub-micron fluid flow simulations.     

Dissipative particle dynamics simulations for fibre suspensions in newtonian and viscoelastic fluids

A versatile model of fibre suspensions in Newtonian and viscoelastic fluids has been developed using dissipative particle dynamics method. The viscoelastic fluid is modelled by linear chains with linear connector spring force (the Oldroyd-B model), which is known to be a reasonable model for the so-called Boger fluid (a dilute suspension of polymer in a highly viscous solvent). The numerical results are in excellent agreement with the analytical results of the Oldroyd-B model in simple shear flow. An effective meso-scale model of fibre in DPD is proposed and then incorporated with simple Newtonian fluid and our Boger fluid to enable entirely study rheological properties of fibre suspensions in both Newtonian and viscoelastic solvents. The numerical results are well compared with available experimental data and other numerical models.     

Direct position determination in the presence of model errors—known waveforms

The performance of the direct position determination (DPD) approach in the presence of model errors is examined. DPD was recently introduced as a promising technique for localization of multiple radio frequency emitters with superior accuracy under low signal-to-noise ratio conditions. We analyze the performance of DPD in the presence of model errors caused by multipath, calibration errors, mutual coupling, etc. The analysis is general enough to encapsulate various sources of errors. Monte Carlo simulations are used to validate the analysis. We show that in many cases of interest DPD should be selected as the preferred method of localization.     

A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach

New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6–8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all-atom simulations. Our average tilt results are also in agreement with all-atom simulations for the case of dense systems.     

Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels

We review recent dissipative particle dynamics (DPD) simulations of electrolyte flow in nanochannels. A method is presented by which the slip length δB at the channel boundaries can be tuned systematically from negative to infinity by introducing suitably adjusted wall-fluid friction forces. Using this method, we study electroosmotic flow (EOF) in nanochannels for varying surface slip conditions and fluids of different ionic strength. Analytic expressions for the flow profiles are derived from the Stokes equation, which are in good agreement with the numerical results. Finally, we investigate the influence of EOF on the effective mobility of polyelectrolytes in nanochannels. The relevant quantity characterizing the effect of slippage is found to be the dimensionless quantity κδB, where 1/κ is an effective electrostatic screening length at the channel boundaries.     

基于Intel MIC平台大规模耗散粒子动力学模拟的设计与优化

耗散粒子动力学(DPD)模拟是一种重要的研究流体动力学特性的计算模拟方法,基于Intel MIC平台设计实现了面向大规模耗散粒子动力学模拟,充分结合了DPD模拟本身的特性和MIC平台的特征。对DPD模拟中的近邻列表构建和短程作用力关键代码实现了向量化优化,在CPU和MIC协处理器之间采用任务计算负载平衡机制,支持MPI进程内线程数量负载平衡控制。分别在原型程序上和LAMMPS集成中做了性能对比分析,实验结果显示了引入相关优化技术的有效性,为进一步研究面向MIC众核平台的分子动力学相关工作奠定了基础。     

Phase diagrams of confined solutions of dimyristoylphosphatidylcholine (DMPC) lipid and cholesterol in nanotubes

We have studied equilibrium morphologies of dimyristoylphosphatidylcholine lipid solution and cholesterol solution confined to nanotubes using dissipative particle dynamics (DPD) simulations. Phase diagrams regarding monomer concentration c versus radius of nanotube r for both solutions are attained. Three types of the inner surface of nanotubes, namely hydrophobic, hydrophilic, and hydroneutral are considered in the DPD simulations. A number of phases and molecular assemblies for the confined solutions are revealed, among others, such as the spiral wetting and bilayer helix. Several phases and assemblies have not been reported in the literature, and some are non-existence in bulk solutions. The ability to control the morphologies and self-assemblies within nanoscale confinement can be exploited for patterning interior surface of nanochannels for application in nanofluidics and nanomedical devices.     

The aggregation and diffusion of asphaltenes studied by GPU-accelerated dissipative particle dynamics

The heavy crude oil consists of thousands of compounds and much of them have large molecular weights and complex structures. Studying the aggregation and diffusion behavior of asphaltenes can facilitate the understanding of the heavy crude oil. In previous studies, the fused aromatic rings were treated as rigid bodies so that dissipative particle dynamics (DPD) integrated with the quaternion method can be used to study asphaltene systems. In this work, DPD integrated with the quaternion method is implemented on graphics processing units (GPUs). Compared with the serial program, tens of times speedup can be achieved when simulations performed on a single GPU. Using multiple GPUs can provide faster computation speed and more storage space for simulations of significant large systems. By using large systems, simulations of the asphaltene–toluene system at extremely dilute concentrations can be performed. The determined diffusion coefficients of asphaltenes are similar to that in experimental studies. At last, the aggregation behavior of asphaltenes in heptane was investigated, and the simulation results agreed with the modified Yen model. Monomers, nanoaggregates and clusters were observed from the simulations at different concentrations.     

Sampled‐data control of networked nonlinear systems with variable delays and drops

This paper investigates the stabilization problem of the nonlinear networked control systems (NCSs) with drops and variable delays. The NCS is modeled as a sampled‐data system. For such a sampled‐data NCS, the stability properties are studied for delay that can be both shorter and longer than one sampling period, respectively. The exponential stability conditions are derived in terms of the parameters of the plant and time delay. On the other hand, a model‐based control scheme based on an approximate discrete‐time model of the plant is presented to guarantee the stability of the closed‐loop system subject to variable time delays and packet losses. The performance of the proposed control schemes are examined through numerical simulations of an automated rendezvous and docking of spacecraft system. Moreover, the simulations show that by employing the model‐based controller, a higher closed‐loop control performance can be achieved. Copyright © 2013 John Wiley & Sons, Ltd.     

AC electroosmotic flow in a DNA concentrator

Experimental velocity measurements are conducted in an AC electrokinetic DNA concentrator. The DNA concentrator is based upon Wong et al. (Transducers 2003, Boston, pp 20–23, 2003a; Anal Chem 76(23):6908–6914, 2004)and consists of two concentric electrodes that generate AC electroosmotic flow to stir the fluid, and dielectrophoretic and electrophoretic force fields that trap DNA near the centre of the inside electrode. A two-colour micro-PIV technique is used to measure the fluid velocity without a priori knowledge of the electric field in the device or the electrical properties of the particles. The device is also simulated computationally. The results indicate that the numerical simulations agree with experimental data in predicting the velocity field structure, except that the velocity scale is an order of magnitude higher for the simulations. Simulation of the dielectrophoretic forces allows the motion of the DNA within the device to be studied. It is suggested that the simulations can be used to study the phenomena occurring in the device, but that experimental data is required to determine the practical conditions under which these phenomena occur.     

A new algorithm for simulating flows of conducting fluids in the presence of electric fields

We propose an algorithm based on dissipative particle dynamics (DPD) for simulations of conducting fluids in the presence of an electric field. In this model, the electrostatic equations are solved in each DPD time step to determine the charge density at the fluid surfaces. These surface charges are distributed on a thin layer of fluid particles near the interface, and the corresponding interfacial electric forces are added to other DPD forces. The algorithm is applied to the electrospinning process at the Taylor cone formation stage. It is shown that, when the applied voltage is sufficiently high, the algorithm captures the formation of a Taylor cone with analytical apex angle 98.6°. Our results demonstrate the potential of the presented DPD algorithm for simulating two-phase problems in the presence of an electric field with non-periodic boundary conditions.     

Robust estimation of nonlinear constitutive law from static equilibrium data for modeling the mechanics of DNA

Long length-scale structural deformations of DNA play a central role in many biological processes including gene expression. The elastic rod model, which uses a continuum approximation, has emerged as a viable tool to model deformations of several biofilaments including DNA molecules. The elastic rod model predictions are however very sensitive to the model of constitutive law (material properties) of the molecule. Robust estimation of the constitutive law from experimental data and feasible molecular dynamics simulations remains a significant challenge. In this paper, we develop a two-step technique to use elastic rod model equations in combination with limited data to estimate the nonlinear constitutive law governing DNA molecules. We first cast the elastic rod model equations in state-space form and express the effect of the unknown constitutive law as an unknown input to the system. We then describe the two-step technique to estimate the unknown constitutive law. Finally, we investigate the robustness of this technique through simulations and discuss various generalizations.     

Daily mobility patterns of small business owners and homeworkers in post-industrial cities

The rise of small businesses, self-employment, and homeworking are transforming traditional industrial ways of working. Our research fills a noticeable gap in the literature by using portable devices (i.e., smartphones) to capture individual mobility data on an understudied population group – small business owners (owner managers and self-employed with up to 49 employees) and whether they work from home in comparison with employees who work at their employer's premises or partly or mainly from home. We recorded week-long individual GPS data on 702 participants and derived a set of measures of daily mobility (number of trips, trip duration, trip distance, and maximum distance from home). Each measure is modelled against a range of individual and neighbourhood-level covariates. Our findings contrast with existing studies that suggest homeworking or self-employment may be associated with lower levels of daily mobility or with compensatory effects between work and non-work travel. Overall, our study points to higher levels of daily mobility of owners of small businesses and the self-employed in cities as they travel longer distances. Further, some homeworkers have on aggregate longer daily trip distances than ‘traditional’ premise-based employees. Most striking, female home-based business owners fall into this group. If homeworking is here to stay after the COVID-19 pandemic, we may see both increases and/or decreases of daily mobility depending on worker types and gender.     

重质油中的分子聚集结构及其对重质油稳定性的影响

重质油组分分子的聚集是重质油最显著的特征之一,重质油的高粘特性和相态稳定性均与此聚集行为有紧密的联系.为克服实验研究获得重质油微观聚集结构的困难,本文采用Zhang等人针对重质油体系改进的耗散粒子动力学(DPD)方法,研究重质油的分子聚集结构及其对重质油稳定性的影响.根据重质油组分的结构特征,可将重质油表达为其他轻组分...     

Modeling and analysis of DNA replication

DNA replication is an important process in the life of a cell. It has to be completed with extreme accuracy in a specific phase of the cell cycle, known as the S phase. Eukaryotic DNA replication is a rather complex and uncertain process. Several mathematical models have been recently proposed in the literature to interpret experimental data from various organisms. A common concern of many of these models is the so-called random gap problem, the observation that eukaryotic DNA replication should last longer than experimental evidence suggests due to its stochastic nature. One of the biological hypotheses proposed for resolving the random gap problem postulates the presence of a limiting factor regulating the rate with which DNA replication initiates. We show how this hypothesis can be captured in the Piecewise Deterministic Markov Process modeling framework. Monte Carlo simulations allow us to analyze the proposed model and compare model predictions with independent experimental data.