Rotational Brownian Dynamics simulations of clathrin cage formation
International Nuclear Information System (INIS)
The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage
Fast simulation of Brownian dynamics in a crowded environment
Smith, Stephen; Grima, Ramon
2016-01-01
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics simulations, however these methods are extremely slow owing to the sheer number of p...
Diffusion of Particle in Hyaluronan Solution, a Brownian Dynamics Simulation
Takasu, Masako; Tomita, Jungo
2004-04-01
Diffusion of a particle in hyaluronan solution is investigated using Brownian dynamics simulation. The slowing down of diffusion is observed, in accordance with the experimental results. The temperature dependence of the diffusion is calculated, and a turnover is obtained when the temperature is increased.
Fast simulation of Brownian dynamics in a crowded environment
Smith, Stephen
2016-01-01
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics simulations, however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous "crowder-free" method to dramatically increase simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the case where the reactive particles are point particles, and where they themselves occupy a volume. We use simulations of simple chemical reaction networks to confirm that our simplification is just as accurate as the original algorithm, and that it corresponds to a large spee...
Brownian dynamics simulations with hard-body interactions: Spherical particles
Behringer, Hans; 10.1063/1.4761827
2012-01-01
A novel approach to account for hard-body interactions in (overdamped) Brownian dynamics simulations is proposed for systems with non-vanishing force fields. The scheme exploits the analytically known transition probability for a Brownian particle on a one-dimensional half-line. The motion of a Brownian particle is decomposed into a component that is affected by hard-body interactions and into components that are unaffected. The hard-body interactions are incorporated by replacing the affected component of motion by the evolution on a half-line. It is discussed under which circumstances this approach is justified. In particular, the algorithm is developed and formulated for systems with space-fixed obstacles and for systems comprising spherical particles. The validity and justification of the algorithm is investigated numerically by looking at exemplary model systems of soft matter, namely at colloids in flow fields and at protein interactions. Furthermore, a thorough discussion of properties of other heurist...
Brownian dynamics simulation for modeling ion permeation across bionanotubes.
Krishnamurthy, Vikram; Chung, Shin-Ho
2005-03-01
The principles underlying Brownian dynamics (BD), its statistical consistency, and algorithms for practical implementation are outlined here. The ability to compute current flow across ion channels confers a distinct advantage to BD simulations compared to other simulation techniques. Thus, two obvious applications of BD ion channels are in calculation of the current-voltage and current-concentration curves, which can be directly compared to the physiological measurements to assess the reliability of the model and predictive power of the method. We illustrate how BD simulations are used to unravel the permeation dynamics in two biological ion channels-the KcsA K+ channel and CIC Cl- channel. PMID:15816176
Active microrheology of Brownian suspensions via Accelerated Stokesian Dynamics simulations
Chu, Henry; Su, Yu; Gu, Kevin; Hoh, Nicholas; Zia, Roseanna
2015-11-01
The non-equilibrium rheological response of colloidal suspensions is studied via active microrheology utilizing Accelerated Stokesian Dynamics simulations. In our recent work, we derived the theory for micro-diffusivity and suspension stress in dilute suspensions of hydrodynamically interacting colloids. This work revealed that force-induced diffusion is anisotropic, with qualitative differences between diffusion along the line of the external force and that transverse to it, and connected these effects to the role of hydrodynamic, interparticle, and Brownian forces. This work also revealed that these forces play a similar qualitative role in the anisotropy of the stress and in the evolution of the non-equilibrium osmotic pressure. Here, we show that theoretical predictions hold for suspensions ranging from dilute to near maximum packing, and for a range of flow strengths from near-equilibrium to the pure-hydrodynamic limit.
Brownian dynamics simulations of ellipsoidal magnetizable particle suspensions
Torres-Díaz, I.; Rinaldi, C.
2014-06-01
The rotational motion of soft magnetic tri-axial ellipsoidal particles suspended in a Newtonian fluid has been studied using rotational Brownian dynamics simulations by solving numerically the stochastic angular momentum equation in an orientational space described by the quaternion parameters. The model is applicable to particles where the effect of shape anisotropy is dominant. The algorithm quantifies the magnetization of a monodisperse suspension of tri-axial ellipsoids in dilute limit conditions under applied constant and time-varying magnetic fields. The variation of the relative permeability with the applied magnetic field of the particle's bulk material was included in the simulations. The results show that the equilibrium magnetization of a suspension of magnetizable tri-axial ellipsoids saturates at high magnetic field amplitudes. Additionally, the dynamic susceptibility at low magnetic field intensity presents a peak in the out-of-phase component, which is significantly smaller than the in-phase component and depends on the Langevin parameter. The dynamic magnetization of the particle suspension is in phase with the magnetic field at low and high frequencies far from the peak of the out-of-phase component.
Magnetoviscosity in dilute ferrofluids from rotational brownian dynamics simulations.
Soto-Aquino, D; Rinaldi, C
2010-10-01
Ferrofluids are suspensions of magnetic nanoparticles which respond to imposed magnetic fields by changing their viscosity without losing their fluidity. Prior work on modeling the behavior of ferrofluids has focused on using phenomenological suspension-scale continuum equations. A disadvantage of this approach is the controversy surrounding the equation describing the rate of change of the ferrofluid magnetization, the so-called magnetization relaxation equation. In this contribution the viscosity of dilute suspensions of spherical magnetic nanoparticles suspended in a Newtonian fluid and under applied shear and constant magnetic fields is studied through rotational brownian dynamics simulations. Simulation results are compared with the predictions of suspension-scale models based on three magnetization relaxation equations. Excellent agreement is observed between simulation results and the predictions of an equation due to Martsenyuk, Raikher, and Shliomis. Good qualitative agreement is observed with predictions of other equations, although these models fail to accurately predict the magnitude and shear rate dependence of the magnetic-field-dependent effective viscosity. Finally, simulation results over a wide range of conditions are collapsed into master curves using a Mason number defined based on the balance of hydrodynamic and magnetic torques. PMID:21230393
International Nuclear Information System (INIS)
Simultaneous orthokinetic and perikinetic coagulations (SOPCs) are studied for small and large Peclet numbers (Pe) using Brownian dynamics simulation. The results demonstrate that the contributions of the Brownian motion and the shear flow to the overall coagulation rate are basically not additive. At the early stages of coagulation with small Peclet numbers, the ratio of overall coagulation rate to the rate of pure perikinetic coagulation is proportional to Pe1/2, while with high Peclet numbers, the ratio of overall coagulation rate to the rate of pure orthokinetic coagulation is proportional to Pe−1/2. Moreover, our results show that the aggregation rate generally changes with time for the SOPC, which is different from that for pure perikinetic and pure orthokinetic coagulations. By comparing the SOPC with pure perikinetic and pure orthokinetic coagulations, we show that the redistribution of particles due to Brownian motion can play a very important role in the SOPC. In addition, the effects of redistribution in the directions perpendicular and parallel to the shear flow direction are different. This perspective explains the behavior of coagulation due to the joint effects of the Brownian motion (perikinetic) and the fluid motion (orthokinetic). (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)
Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
Lipková, Jana
2011-01-01
A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-bcȳ model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6(2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated. © 2011 Society for Industrial and Applied Mathematics.
Brownian dynamics in a confined geometry. Experiments and numerical simulations
Garnier, Nicolas; Ostrowsky, N.
1991-01-01
The Brownian dynamics of a colloidal suspension is measured in the immediate vicinity of a rigid surface by the Evanescent Quasielastic Light Scattering Technique. A net decrease of the measured diffusion coefficient is observed, due to the hydrodynamic slowing down of the particles very close to the wall. This effect is all the more important when the particles are allowed to get closer to the wall, i.e. when the range of the static wall/particle repulsive interaction decreases. It thus prov...
Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics
Erban, Radek
2015-01-01
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.
Jung, Jiyun; Lee, Jumin; Kim, Jun Soo
2015-03-01
We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.
A comparison of lattice-Boltzmann and Brownian dynamics simulations of dilute polymer solutions
Ladd, Tony; Kekre, Rahul; Butler, Jason
2008-11-01
We have compared lattice-Boltzmann and Brownian dynamics simulations of a single flexible polymer, in isolation and in confined geometries. In the case of the isolated chain we find agreement to within 1% in the diffusion coefficient and the Rouse mode relaxation times. We have obtained good agreement for the concentration profiles in a bounded shear flow, but the Brownian dynamics simulations currently use a superposition of the hydrodynamic fields generated by the walls. We expect to know the effects of the inter-wall correction by the time of the meeting. We have gone to some lengths to match the conditions of both simulations as closely as possible. We use identical potential parameters and correct for the differences between the periodic boundaries used in the LB simulations and the unbounded domains used in the BD simulations. We use very long runs, of the order of 10000 times the longest relaxation time, to reduce the statistical uncertainties to less than 0.1%. We find excellent agreement in the relaxation times over a wide range of temperatures and fluid viscosity. The most quantitative agreement is achieved in the weak coupling limit, where the hydrodynamic radius of the monomers is less than one quarter of the lattice spacing.
Matrix-free Brownian dynamics simulation technique for semidilute polymeric solutions
Saadat, Amir; Khomami, Bamin
2015-09-01
Evaluating the concentration dependence of static and dynamic properties of macromolecules in semidilute polymer solutions requires accurate calculation of long-range hydrodynamic interactions (HI) and short range excluded volume (EV) forces. In conventional Brownian dynamics simulations (BDS), computation of HI necessitates construction of a dense diffusion tensor commonly performed via Ewald summation. Krylov subspace techniques allow efficient decomposition of this tensor [computational cost scales as O (N2) , where N is the total number of beads in bead-spring representation of macromolecules in a simulation box] and computation of Brownian displacements in the box. In this paper, a matrix-free approach for calculation of HI is implemented which leads to O (N logN ) scaling of computational expense. The fidelity of the algorithm is demonstrated by evaluating the asymptotic value of center-of-mass diffusivity of polymer molecules at very low concentrations and their radius of gyration scaling as a function of number of beads for dilute and semidilute solutions (with concentrations up to 5 times the overlap concentration). In turn, a favorable comparison between our results and the blob theory is shown.
Chun, Myung-Suk; Kim, Chongyoup; Lee, Duck E.
2009-05-01
In our recent Brownian dynamics (BD) simulation study, the structure and dynamics of anionic polyelectrolyte xanthan in bulk solution as well as confined spaces of slitlike channel were examined by applying a coarse-grained model with nonlinear bead-spring discretization of a whole chain [J. Jeon and M.-S. Chun, J. Chem. Phys. 126, 154904 (2007)]. This model goes beyond other simulations as they did not consider both long-range electrostatic and hydrodynamic interactions between pairs of beads. Simulation parameters are obtained from the viscometric method of rheology data on the native and sonicated xanthan polysaccharides, which have a contour length less than 1μm . The size of the semiflexible polyelectrolyte can be well described by the wormlike chain model once the electrostatic effects are taken into account by the persistence length measured at a long length scale. For experimental verifications, single molecule visualization was performed on fluorescein-labeled xanthan using an inverted fluorescence microscope, and the motion of an individual molecule was quantified. Experimental results on the conformational changes in xanthan chain in the electrolyte solution have a reasonable trend to agree with the prediction by BD simulations. In the translational diffusion induced by the Debye screening effect, the simulation prediction reveals slightly higher values compared to those of our measurements, although it agrees with the literature data. Considering the experimental restrictions, our BD simulations are verified to model the single polyelectrolyte well.
DNA electrophoresis in tri-block copolymer gels--experiments and Brownian dynamics simulation
Wei, Ling; van Winkle, David H.
2015-03-01
The mobility of double-stranded DNA ladders in Pluronics®P105, P123 and F127, was measured by two-dimensional gel electrophoresis. Pluronics®are triblock copolymers which form gel-like phases of micelles arranged with cubic order at room temperature. A 10 base pair and a 25 base pair DNA ladder were used as samples in gel electrophoresis. The monotonically decreasing mobility with increasing length observed in the agarose separations is not observed in separations in Pluronics®. Rather, a complicated dependence of mobility on DNA length is observed, where mobility vs. length increases for short DNA molecules then decreases for longer molecules. There is also a variation of mobility with length correlated to the micelle diameter. Brownian dynamics simulations of a discrete wormlike chain model were performed to simulate short DNA molecules migrating in free solution and in a face-centered cubic matrix. By incorporating hydrodynamic interactions, the trend of simulated length-dependent mobility qualitatively agrees with experimental measurements.
Cook, Sara Iliafar
T, respectively). In addition to the binding strength of ssDNA nucleotide to surfaces, it is equally as important to understand the dynamics of these interactions. The force response of a simple chain-like polymeric molecule (representative of single stranded DNA) was studied using Brownian dynamics to shed light on these dynamics and the features that may be masked in SMFS experiments. Through simulations at slow peeling rates, our Brownian dynamics model confirmed the predictions of an equilibrium statistical thermodynamic model. Faster removal rates resulted in deviations from equilibrium which were dominated by a combination of Stokes (viscous) drag and a finite desorption rate of the monomeric units. Furthermore, the force probe's thermal fluctuations were shown to be affected by the spring constant of the contact mode AFM cantilever Consequently, this effect provided evidence on the source of disappearance for certain key features such as force spikes, associated with the desorption of individual links and predicted by the statistical thermodynamic model under displacement control, from SMFS experiments. In studying the elastic response of a freely jointed chain stretched in 2D and 3D, we obtained analytical expressions for two modes of stretching: i) when force is applied only to one end of the chain, and ii) when the applied force is distributed uniformly throughout the chain. By comparing, we confirmed that these expressions correctly predict the results obtained from our Brownian dynamics simulations as well as experimental results from the literature.
LI Minghai; Liu, Yongsheng; Bansil, Rama
2010-01-01
The kinetics of the transformation from the hexagonal packed cylinder (HEX) phase to the face-centered-cubic (FCC) phase was simulated using Brownian Dynamics for an ABA triblock copolymer in a selective solvent for the A block. The kinetics was obtained by instantaneously changing either the temperature of the system or the well-depth of the Lennard-Jones potential. Detailed analysis showed that the transformation occurred via a rippling mechanism. The simulation results indicated that the o...
Soto-Aquino, D; Rosso, D; Rinaldi, C
2011-11-01
Ferrofluids are colloidal suspensions of magnetic nanoparticles that exhibit normal liquid behavior in the absence of magnetic fields but respond to imposed magnetic fields by changing their viscosity without loss of fluidity. The response of ferrofluids to constant shear and magnetic fields has received a lot of attention, but the response of ferrofluids to oscillatory shear remains largely unexplored. In the present work we used rotational Brownian dynamics to study the dynamic properties of ferrofluids with thermally blocked nanoparticles under oscillatory shear and constant magnetic fields. Comparisons between simulations and modeling using the ferrohydrodynamics equations were also made. Simulation results show that, for small rotational Péclet number, the in-phase and out-of-phase components of the complex viscosity depend on the magnitude of the magnetic field and frequency of the shear, following a Maxwell-like model with field-dependent viscosity and characteristic time equal to the field-dependent transverse magnetic relaxation time of the nanoparticles. Comparison between simulations and the numerical solution of the ferrohydrodynamic equations shows that the oscillatory rotational magnetoviscosity for an oscillating shear field obtained using the kinetic magnetization relaxation equation quantitatively agrees with simulations for a wide range of Péclet number and Langevin parameter but has quantitative deviations from the simulations at high values of the Langevin parameter. These predictions indicate an apparent elastic character to the rheology of these suspensions, even though we are considering the infinitely dilute limit in which there are negligible particle-particle interactions and, as such, chains do not form. Additionally, an asymptotic analytical solution of the ferrohydrodynamics equations, valid for Peferrofluids under conditions of small shear rates. At higher shear rates the Cox-Merz rule ceases to apply. PMID:22181497
Sánchez, J H; Rinaldi, C
2009-03-15
The magnetic field dependent viscosity (magnetoviscosity) of dilute suspensions of magnetic tri-axial ellipsoidal particles suspended in a Newtonian fluid and under applied shear and magnetic fields was studied numerically. Brownian dynamics simulations were performed to compute the intrinsic magnetoviscosity of the suspension. Results are presented for the response of dilute suspensions of ellipsoidal particles to constant magnetic and shear flow fields. Suspensions of ellipsoidal particles show a significant effect of aspect ratio on the intrinsic magnetoviscosity of the suspension, and this effect is more pronounced as the aspect ratio becomes more extreme. The use of an effective rotational diffusion coefficient D(r,eff) collapses the normalized intrinsic magnetoviscosity of all suspensions to a master curve as a function of Péclet number with the Langevin parameter alpha=(mu(0)muH)/(k(B)T) as parameter, up to a critical value of alpha for which the results for suspensions of spherical particles deviate from those of suspensions of ellipsoids. This discrepancy is attributed to the action of the shear-torque on the ellipsoidal particles, which tends to orient these particles in the direction of maximum deformation of the simple shear flow, and which does not act on spherical particles. PMID:19100560
Markutsya, Sergiy; Fox, Rodney; Vigil, Dennis; Subramaniam, Shankar
2009-11-01
Nanoparticle synthesis in turbulent reactors subjects anoparticle aggregates to a homogeneous, time-varying shear flow. The shear flow results in anisotropic clusters and it is of interest to characterize the structural properties of these clusters and their effects on initiation and acceleration of aggregation, the restructuring of clusters, and their breakage. The anisotropic structure of a sheared cluster is characterized by the ratio of the major to minor axis length of the approximating ellipsoid oriented along the cluster moment of inertia tensor's principal axes. Brownian dynamics simulations show that shear flow dramatically changes the structure of aggregates by initiating the formation of more compact structures at smaller length scales perpendicular to the shear direction, and anisotropic, cigar--like structures along the shear direction. More compact clusters correspond to higher local volumetric potential energy density. Therefore, we classify the compactness and anisotropy of sheared clusters on a map of local volumetric potential energy density versus ratio of the principal values of the cluster's moment of inertia tensor. The effect of shear on breakage of clusters is characterized by the radius of gyration Rg^cr of the largest stable aggregate for a given value of the imposed steady shear rate (P'eclet number).
Brownian Dynamics Simulation of two-dimensional nanosheets under extensional flow
Xu, Yueyi; Green, Micah
2014-11-01
We investigated the morphology change of two-dimensional nanosheets under extensional flow using a coarse-grained model. Nanosheets such as graphene are promising materials for a variety of materials and electronics applications; extensional flow fields are used to cast or process liquid nanosheet dispersions in several processing techniques, including spin coating and compression molding. Process parameters, including bending stiffness and Weissenberg numbers can have a significant impact on the nanosheet morphology and the physical properties of the finished products. We use Brownian Dynamics simulations to study the impact of external flow field on a two-dimensional bead-rod lattice model. Our model was previously demonstrated for steady shear flow. Here we studied the change of morphology of graphene over time and varied the sheet size, bending stiffness and Weissenberg number. Our results showed a flattening behavior that increases with Weissenberg number. Our results also showed significant differences between nanosheets as a function of bending stiffness, with contrasting ``plate'' and ``washrag'' results under extension. The intrinsic viscosity first experiences a drop with Weissenberg number followed by a plateau associated with maximum extension.
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
GPU accelerated Monte Carlo simulation of Brownian motors dynamics with CUDA
Spiechowicz, J; Machura, L
2014-01-01
This work presents an updated and extended guide on methods of a proper acceleration of the Monte Carlo integration of stochastic differential equations with the commonly available NVIDIA Graphics Processing Units using the CUDA programming environment. We outline the general aspects of the scientific computing on graphics cards and demonstrate them with two models of a well known phenomenon of the noise induced transport of Brownian motors in periodic structures. As a source of fluctuations in the considered systems we selected the three most commonly occurring noises: the Gaussian white noise, the white Poissonian noise and the dichotomous process also known as a random telegraph signal. The detailed discussion on various aspects of the applied numerical schemes is also presented. The measured speedup can be of the astonishing order of 2000 when compared to a typical CPU. This number significantly expands the range of problems solvable by use of stochastic simulations, allowing even an interactive research ...
International Nuclear Information System (INIS)
An understanding of particle transport is necessary to reduce contamination of semiconductor wafers during low-pressure processing. The trajectories of particles in these reactors are determined by external forces (the most important being neutral fluid drag, thermophoresis, electrostatic, viscous ion drag, and gravitational), by Brownian motion (due to neutral and charged gas molecule collisions), and by particle inertia. Gas velocity and temperature fields are also needed for particle transport calculations, but conventional continuum fluid approximations break down at low pressures when the gas mean free path becomes comparable to chamber dimensions. Thus, in this work we use a massively parallel direct simulation Monte Carlo method to calculate low-pressure internal gas flow fields which show temperature jump and velocity slip at the reactor boundaries. Because particle residence times can be short compared to particle response times in these low-pressure systems (for which continuum diffusion theory fails), we solve the Langevin equation using a numerical Lagrangian particle tracking model which includes a fluctuating Brownian force. Because of the need for large numbers of particle trajectories to ensure statistical accuracy, the particle tracking model is also implemented on a massively parallel computer. The particle transport model is validated by comparison to the Ornstein endash Furth theoretical result for the mean square displacement of a cloud of particles. For long times, the particles tend toward a Maxwellian spatial distribution, while at short times, particle spread is controlled by their initial (Maxwellian) velocity distribution. Several simulations using these techniques are presented for particle transport and deposition in a low pressure, parallel-plate reactor geometry. The corresponding particle collection efficiencies on a wafer for different particle sizes, gas temperature gradients, and gas pressures are evaluated
Li, Minghai; Bansil, Rama
2010-01-01
The kinetics of the transformation from the hexagonal packed cylinder (HEX) phase to the face-centered-cubic (FCC) phase was simulated using Brownian Dynamics for an ABA triblock copolymer in a selective solvent for the A block. The kinetics was obtained by instantaneously changing either the temperature of the system or the well-depth of the Lennard-Jones potential. Detailed analysis showed that the transformation occurred via a rippling mechanism. The simulation results indicated that the order-order transformation (OOT) was a nucleation and growth process when the temperature of the system instantly jumped from 0.8 to 0.5. The time evolution of the structure factor obtained by Fourier Transformation showed that the peak intensities of the HEX and FCC phases could be fit well by an Avrami equation.
Energy Technology Data Exchange (ETDEWEB)
Mereghetti, Paolo; Wade, Rebecca C.
2012-07-26
High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.
Theers, Mario; Westphal, Elmar; Gompper, Gerhard; Winkler, Roland G.
2016-03-01
The friction and diffusion coefficients of rigid spherical colloidal particles dissolved in a fluid are determined from velocity and force autocorrelation functions by mesoscale hydrodynamic simulations. Colloids with both slip and no-slip boundary conditions are considered, which are embedded in fluids modeled by multiparticle collision dynamics with and without angular momentum conservation. For no-slip boundary conditions, hydrodynamics yields the well-known Stokes law, while for slip boundary conditions the lack of angular momentum conservation leads to a reduction of the hydrodynamic friction coefficient compared to the classical result. The colloid diffusion coefficient is determined by integration of the velocity autocorrelation function, where the numerical result at shorter times is combined with the theoretical hydrodynamic expression for longer times. The suitability of this approach is confirmed by simulations of sedimenting colloids. In general, we find only minor deviations from the Stokes-Einstein relation, which even disappear for larger colloids. Importantly, for colloids with slip boundary conditions, our simulation results contradict the frequently assumed additivity of local and hydrodynamic diffusion coefficients.
Mohammadi, Maziar; Larson, Eric D.; Liu, Jun; Larson, Ronald G.
2015-01-01
Brownian dynamics simulations are performed to study the binding kinetics in the dilute-sphere limit by considering interactions of two spheres under shear flow across the entire range of Peclet numbers, spanning both perikinetic (diffusion-controlled) and orthokinetic (flow-controlled) coagulation regimes. The dilute regime is attained by carrying out two-sphere simulations in periodic boxes of different sizes and aspect ratios and extrapolating toward the infinite box limit. Effects of particle type (Janus and isotropic particles), shear rate, hydrodynamic interactions, and inter-particle potential are explored. We find that rectangular boxes with appropriate aspect ratios overcome a particle "shadow effect" that cannot be overcome with cubic boxes unless huge boxes are used. With rectangular boxes, we obtain converged binding kinetics for the whole Peclet number range, while cubic boxes of increasing size allow converged results only in the absence of flow. We consider the effect of binding both in a secondary minimum controlled by a combination of electrostatic repulsion and depletion attraction, as well as in a primary minimum governed by induced-dipole attraction. Results are computed using both realistic interaction potentials and by replacing the potential with a simple cutoff gap distance at which binding is deemed to occur. Results agree with several existing reports including Smoluchowski predictions in the zero- and infinite-shear-rate limits, and high-Pe perturbation results of Feke and Schowalter [J. Fluid Mech. 133, 17-35 (1983)] at Peclet numbers (Pe) above 100. Finally, we compute binding times for anisotropic Janus particles which have both repulsive and attractive faces, for a wide range of Pe number.
Brownian Dynamics of charged particles in a constant magnetic field
Hou, L J; Piel, A; Shukla, P K
2009-01-01
Numerical algorithms are proposed for simulating the Brownian dynamics of charged particles in an external magnetic field, taking into account the Brownian motion of charged particles, damping effect and the effect of magnetic field self-consistently. Performance of these algorithms is tested in terms of their accuracy and long-time stability by using a three-dimensional Brownian oscillator model with constant magnetic field. Step-by-step recipes for implementing these algorithms are given in detail. It is expected that these algorithms can be directly used to study particle dynamics in various dispersed systems in the presence of a magnetic field, including polymer solutions, colloidal suspensions and, particularly complex (dusty) plasmas. The proposed algorithms can also be used as thermostat in the usual molecular dynamics simulation in the presence of magnetic field.
Brownian shape dynamics in fission
Randrup Jørgen; Möller Peter
2013-01-01
It was recently shown that remarkably accurate fission-fragment mass distributions are obtained by treating the nuclear shape evolution as a Brownian walk on previously calculated five-dimensional potentialenergy surfaces; the current status of this novel method is described here.
Brownian shape dynamics in fission
Directory of Open Access Journals (Sweden)
Randrup Jørgen
2013-12-01
Full Text Available It was recently shown that remarkably accurate fission-fragment mass distributions are obtained by treating the nuclear shape evolution as a Brownian walk on previously calculated five-dimensional potentialenergy surfaces; the current status of this novel method is described here.
Babaei, Hasan; Keblinski, Pawel; Khodadadi, J. M.
2013-02-01
It has been recently demonstrated through experiments that the observed high enhancements in thermal conductivity of nanofluids are due to aggregation of nanoparticles rather than the previously stated mechanism of the Brownian motion-induced micro-convection. In this paper, we use equilibrium molecular dynamics simulations to investigate the role of micro-convection on the thermal conductivity of well-dispersed nanofluids. We show that while the individual terms in the heat current autocorrelation function associated with nanoparticle diffusion achieve significant values, these terms essentially cancel each other if correctly defined average enthalpy expressions are subtracted. Otherwise, erroneous thermal conductivity enhancements will be predicted, which are attributed to Brownian motion-induced micro-convection. Consequently, micro-convection does not contribute noticeably to the thermal conductivity and the predicted thermal conductivity enhancements are consistent with the effective medium theory.
3-d Brownian dynamics simulations of the smallest units of an active biological material
Luettmer-Strathmann, Jutta; Paudyal, Nabina; Adeli Koudehi, Maral
Motor proteins generate stress in a cytoskeletal network by walking on one strand of the network while being attached to another one. A protein walker in contact with two elements of the network may be considered the smallest unit of an active biological material. In vitro experiments, mathematical modeling and computer simulations have provided important insights into active matter on large and on very small length and time scales. However, it is still difficult to model the effects of local environment and interactions at intermediate scales. Recently, we developed a coarse-grained, three-dimensional model for a motor protein transporting cargo by walking on a substrate. In this work, we simulate a tethered motor protein pulling a substrate with elastic response. As the walker progresses, the retarding force due to the substrate tension increases until contact fails. We present simulation results for the effect of motor-protein activity on the tension in the substrate and the effect of the retarding force on the processivity of the molecular motor.
Energy Technology Data Exchange (ETDEWEB)
Sanchez, Jorge H. [Department of Chemical Engineering, University of Puerto Rico, Mayaguez campus, P.O. Box 9046, Mayaguez, PR 00681 (Puerto Rico); Facultad de Ingenieria Quimica, Universidad Pontificia Bolivariana, Medellin (Colombia); Rinaldi, Carlos [Department of Chemical Engineering, University of Puerto Rico, Mayaguez campus, P.O. Box 9046, Mayaguez, PR 00681 (Puerto Rico)], E-mail: crinaldi@uprm.edu
2009-10-15
The rotational Brownian motion of magnetized tri-axial ellipsoidal particles (orthotropic particles) suspended in a Newtonian fluid, in the dilute suspension limit, under applied d.c. and a.c. magnetic fields was studied using rotational Brownian dynamics simulations. The algorithm describing the change in the suspension magnetization was obtained from the stochastic angular momentum equation using the fluctuation-dissipation theorem and a quaternion formulation of orientation space. Simulation results are in agreement with the Langevin function for equilibrium magnetization and with single-exponential relaxation from equilibrium at small fields using Perrin's effective relaxation time. Dynamic susceptibilities for ellipsoidal particles of different aspect ratios were obtained from the response to oscillating magnetic fields of different frequencies and described by Debye's model for the complex susceptibility using Perrin's effective relaxation time. Simulations at high equilibrium and probe fields indicate that Perrin's effective relaxation time continues to describe relaxation from equilibrium and response to oscillating fields even beyond the small field limit.
Brownian motion on random dynamical landscapes
Suñé Simon, Marc; Sancho, José María; Lindenberg, Katja
2016-03-01
We present a study of overdamped Brownian particles moving on a random landscape of dynamic and deformable obstacles (spatio-temporal disorder). The obstacles move randomly, assemble, and dissociate following their own dynamics. This landscape may account for a soft matter or liquid environment in which large obstacles, such as macromolecules and organelles in the cytoplasm of a living cell, or colloids or polymers in a liquid, move slowly leading to crowding effects. This representation also constitutes a novel approach to the macroscopic dynamics exhibited by active matter media. We present numerical results on the transport and diffusion properties of Brownian particles under this disorder biased by a constant external force. The landscape dynamics are characterized by a Gaussian spatio-temporal correlation, with fixed time and spatial scales, and controlled obstacle concentrations.
Stochastic description of quantum Brownian dynamics
Yan, Yun-An; Shao, Jiushu
2016-08-01
Classical Brownian motion has well been investigated since the pioneering work of Einstein, which inspired mathematicians to lay the theoretical foundation of stochastic processes. A stochastic formulation for quantum dynamics of dissipative systems described by the system-plus-bath model has been developed and found many applications in chemical dynamics, spectroscopy, quantum transport, and other fields. This article provides a tutorial review of the stochastic formulation for quantum dissipative dynamics. The key idea is to decouple the interaction between the system and the bath by virtue of the Hubbard-Stratonovich transformation or Itô calculus so that the system and the bath are not directly entangled during evolution, rather they are correlated due to the complex white noises introduced. The influence of the bath on the system is thereby defined by an induced stochastic field, which leads to the stochastic Liouville equation for the system. The exact reduced density matrix can be calculated as the stochastic average in the presence of bath-induced fields. In general, the plain implementation of the stochastic formulation is only useful for short-time dynamics, but not efficient for long-time dynamics as the statistical errors go very fast. For linear and other specific systems, the stochastic Liouville equation is a good starting point to derive the master equation. For general systems with decomposable bath-induced processes, the hierarchical approach in the form of a set of deterministic equations of motion is derived based on the stochastic formulation and provides an effective means for simulating the dissipative dynamics. A combination of the stochastic simulation and the hierarchical approach is suggested to solve the zero-temperature dynamics of the spin-boson model. This scheme correctly describes the coherent-incoherent transition (Toulouse limit) at moderate dissipation and predicts a rate dynamics in the overdamped regime. Challenging problems
Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics
Franz, Benjamin
2013-06-19
Two algorithms that combine Brownian dynami cs (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented. © 2013 Society for Industrial and Applied Mathematics.
An exact solution to Brownian dynamics of a reversible bimolecular reaction in one dimension
Smith, Stephen; Grima, Ramon
2016-01-01
Brownian dynamics is a popular fine-grained method for simulating systems of interacting particles, such as chemical reactions. Though the method is simple to simulate, it is generally assumed that the dynamics is impossible to solve exactly and analytically, aside from some trivial systems. We here give the first exact analytical solution to a non-trivial Brownian dynamics system: the reaction $A+B\\xrightleftharpoons[]{}C$ in equilibrium in one-dimensional periodic space. The solution is a f...
International Nuclear Information System (INIS)
Static/structural characteristics of non-covalent complexes, formed by terminally charged hyperbranched polymers and oppositely charged neutralizing linear polyelectrolytes, are examined by means of Brownian dynamics computer simulations. Excluded-volume, electrostatic and hydrodynamic interactions are taken into account in implicit solvent. Three pairs of complexes consisting of linear chains and hyperbranched molecules each bearing different molecular weight and distinctly diverse topologies are examined under conditions of varying electrostatic interactions. The findings from the present work demonstrate that through an appropriate modification of internal structure and external stimuli, key attributes of such complexes like size, shape and local density distribution, can be tuned at desired levels, rendering them promising candidates for a wide range of pertinent nanoscale applications
Dynamics and Efficiency of Brownian Rotors
Bauer, Wolfgang R
2008-01-01
Brownian rotors play an important role in biological systems and in future nano-technological applications. However the mechanisms determining their dynamics, efficiency and performance remain to be characterized. Here the F0 portion of the F-ATP synthase is considered as a paradigm of a Brownian rotor. In a generic analytical model we analyze the stochastic rotation of F0-like motors as a function of the driving free energy difference and of the free energy profile the rotor is subjected to. The latter is composed of the rotor interaction with its surroundings, of the free energy of chemical transitions, and of the workload. The dynamics and mechanical efficiency of the rotor depends on the magnitude of its stochastic motion driven by the free energy energy difference and its rectification on the reaction-diffusion path. We analyze which free energy profiles provide maximum flow and how their arrangement on the underlying reaction-diffusion path affects rectification and -- by this -- the efficiency.
Dynamical objectivity in quantum Brownian motion
Tuziemski, J.; Korbicz, J. K.
2015-11-01
Classical objectivity as a property of quantum states —a view proposed to explain the observer-independent character of our world from quantum theory, is an important step in bridging the quantum-classical gap. It was recently derived in terms of spectrum broadcast structures for small objects embedded in noisy photon-like environments. However, two fundamental problems have arisen: a description of objective motion and applicability to other types of environments. Here we derive an example of objective states of motion in quantum mechanics by showing the formation of dynamical spectrum broadcast structures in the celebrated, realistic model of decoherence —Quantum Brownian Motion. We do it for realistic, thermal environments and show their noise-robustness. This opens a potentially new method of studying the quantum-to-classical transition.
An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles
Energy Technology Data Exchange (ETDEWEB)
Ilie, Ioana M.; Briels, Wim J. [Computational Biophysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Otter, Wouter K. den, E-mail: w.k.denotter@utwente.nl [Computational Biophysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)
2015-03-21
Brownian Dynamics is the designated technique to simulate the collective dynamics of colloidal particles suspended in a solution, e.g., the self-assembly of patchy particles. Simulating the rotational dynamics of anisotropic particles by a first-order Langevin equation, however, gives rise to a number of complications, ranging from singularities when using a set of three rotational coordinates to subtle metric and drift corrections. Here, we derive and numerically validate a quaternion-based Rotational Brownian Dynamics algorithm that handles these complications in a simple and elegant way. The extension to hydrodynamic interactions is also discussed.
An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles
International Nuclear Information System (INIS)
Brownian Dynamics is the designated technique to simulate the collective dynamics of colloidal particles suspended in a solution, e.g., the self-assembly of patchy particles. Simulating the rotational dynamics of anisotropic particles by a first-order Langevin equation, however, gives rise to a number of complications, ranging from singularities when using a set of three rotational coordinates to subtle metric and drift corrections. Here, we derive and numerically validate a quaternion-based Rotational Brownian Dynamics algorithm that handles these complications in a simple and elegant way. The extension to hydrodynamic interactions is also discussed
Greives, Nicholas; Zhou, Huan-Xiang
2012-10-01
A method developed by Northrup et al. [J. Chem. Phys. 80, 1517 (1984)], 10.1063/1.446900 for calculating protein-ligand binding rate constants (ka) from Brownian dynamics (BD) simulations has been widely used for rigid molecules. Application to flexible molecules is limited by the formidable computational cost to treat conformational fluctuations during the long BD simulations necessary for ka calculation. Here, we propose a new method called BDflex for ka calculation that circumvents this problem. The basic idea is to separate the whole space into an outer region and an inner region, and formulate ka as the product of kE and bar η _d, which are obtained by separately solving exterior and interior problems. kE is the diffusion-controlled rate constant for the ligand in the outer region to reach the dividing surface between the outer and inner regions; in this exterior problem conformational fluctuations can be neglected. bar η _d is the probability that the ligand, starting from the dividing surface, will react at the binding site rather than escape to infinity. The crucial step in reducing the determination of bar η _d to a problem confined to the inner region is a radiation boundary condition imposed on the dividing surface; the reactivity on this boundary is proportional to kE. By confining the ligand to the inner region and imposing the radiation boundary condition, we avoid multiple-crossing of the dividing surface before reaction at the binding site and hence dramatically cut down the total simulation time, making the treatment of conformational fluctuations affordable. BDflex is expected to have wide applications in problems where conformational fluctuations of the molecules are crucial for productive ligand binding, such as in cases where transient widening of a bottleneck allows the ligand to access the binding pocket, or the binding site is properly formed only after ligand entrance induces the closure of a lid.
Dynamical 3-Space: Anisotropic Brownian Motion Experiment
Cahill R. T.
2015-01-01
In 2014 Jiapei Dai reported evidence of anisotropic Brownian motion of a toluidine blue colloid solution in water. In 2015 Felix Scholkmann analysed the Dai data and detected a sidereal time dependence, indicative of a process driving the preferred Brownian mo- tion diffusion direction to a star-based preferred direction. Here we further analyse the Dai data and extract the RA and Dec of that preferred direction, and relate the data to previous determinations from NASA Spacecr...
Momentum conserving Brownian dynamics propagator for complex soft matter fluids.
Padding, J T; Briels, W J
2014-12-28
We present a Galilean invariant, momentum conserving first order Brownian dynamics scheme for coarse-grained simulations of highly frictional soft matter systems. Friction forces are taken to be with respect to moving background material. The motion of the background material is described by locally averaged velocities in the neighborhood of the dissolved coarse coordinates. The velocity variables are updated by a momentum conserving scheme. The properties of the stochastic updates are derived through the Chapman-Kolmogorov and Fokker-Planck equations for the evolution of the probability distribution of coarse-grained position and velocity variables, by requiring the equilibrium distribution to be a stationary solution. We test our new scheme on concentrated star polymer solutions and find that the transverse current and velocity time auto-correlation functions behave as expected from hydrodynamics. In particular, the velocity auto-correlation functions display a long time tail in complete agreement with hydrodynamics. PMID:25554134
From Brownian Dynamics to Markov Chain: An Ion Channel Example
Chen, Wan
2014-02-27
A discrete rate theory for multi-ion channels is presented, in which the continuous dynamics of ion diffusion is reduced to transitions between Markovian discrete states. In an open channel, the ion permeation process involves three types of events: an ion entering the channel, an ion escaping from the channel, or an ion hopping between different energy minima in the channel. The continuous dynamics leads to a hierarchy of Fokker-Planck equations, indexed by channel occupancy. From these the mean escape times and splitting probabilities (denoting from which side an ion has escaped) can be calculated. By equating these with the corresponding expressions from the Markov model, one can determine the Markovian transition rates. The theory is illustrated with a two-ion one-well channel. The stationary probability of states is compared with that from both Brownian dynamics simulation and the hierarchical Fokker-Planck equations. The conductivity of the channel is also studied, and the optimal geometry maximizing ion flux is computed. © 2014 Society for Industrial and Applied Mathematics.
Van den Broeck, C; Kawai, R
2006-06-01
Onsager symmetry implies that a Brownian motor, driven by a temperature gradient, will also perform a refrigerator function upon loading. We analytically calculate the corresponding heat flow for an exactly solvable microscopic model and compare it with molecular dynamics simulations. PMID:16803223
Studying protein assembly with reversible Brownian dynamics of patchy particles
International Nuclear Information System (INIS)
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly
Long, Hai; Chang, Christopher H; King, Paul W; Ghirardi, Maria L; Kim, Kwiseon
2008-10-01
The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer. PMID:18621810
Brownian dynamics of confined rigid bodies
Energy Technology Data Exchange (ETDEWEB)
Delong, Steven; Balboa Usabiaga, Florencio; Donev, Aleksandar, E-mail: donev@courant.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 (United States)
2015-10-14
We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of the overdamped Langevin equations of motion, one based on the Fixman midpoint method and the other based on a random finite difference approach, both of which ensure that the correct stochastic drift term is captured in a computationally efficient way. We study several examples of rigid colloidal particles diffusing near a no-slip boundary and demonstrate the importance of the choice of tracking point on the measured translational mean square displacement (MSD). We examine the average short-time as well as the long-time quasi-two-dimensional diffusion coefficient of a rigid particle sedimented near a bottom wall due to gravity. For several particle shapes, we find a choice of tracking point that makes the MSD essentially linear with time, allowing us to estimate the long-time diffusion coefficient efficiently using a Monte Carlo method. However, in general, such a special choice of tracking point does not exist, and numerical techniques for simulating long trajectories, such as the ones we introduce here, are necessary to study diffusion on long time scales.
Brownian dynamics of confined rigid bodies
Delong, Steven; Balboa Usabiaga, Florencio; Donev, Aleksandar
2015-10-01
We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of the overdamped Langevin equations of motion, one based on the Fixman midpoint method and the other based on a random finite difference approach, both of which ensure that the correct stochastic drift term is captured in a computationally efficient way. We study several examples of rigid colloidal particles diffusing near a no-slip boundary and demonstrate the importance of the choice of tracking point on the measured translational mean square displacement (MSD). We examine the average short-time as well as the long-time quasi-two-dimensional diffusion coefficient of a rigid particle sedimented near a bottom wall due to gravity. For several particle shapes, we find a choice of tracking point that makes the MSD essentially linear with time, allowing us to estimate the long-time diffusion coefficient efficiently using a Monte Carlo method. However, in general, such a special choice of tracking point does not exist, and numerical techniques for simulating long trajectories, such as the ones we introduce here, are necessary to study diffusion on long time scales.
Solano, Carlos J F; Pothula, Karunakar R; Prajapati, Jigneshkumar D; De Biase, Pablo M; Noskov, Sergei Yu; Kleinekathöfer, Ulrich
2016-05-10
All-atom molecular dynamics simulations have a long history of applications studying ion and substrate permeation across biological and artificial pores. While offering unprecedented insights into the underpinning transport processes, MD simulations are limited in time-scales and ability to simulate physiological membrane potentials or asymmetric salt solutions and require substantial computational power. While several approaches to circumvent all of these limitations were developed, Brownian dynamics simulations remain an attractive option to the field. The main limitation, however, is an apparent lack of protein flexibility important for the accurate description of permeation events. In the present contribution, we report an extension of the Brownian dynamics scheme which includes conformational dynamics. To achieve this goal, the dynamics of amino-acid residues was incorporated into the many-body potential of mean force and into the Langevin equations of motion. The developed software solution, called BROMOCEA, was applied to ion transport through OmpC as a test case. Compared to fully atomistic simulations, the results show a clear improvement in the ratio of permeating anions and cations. The present tests strongly indicate that pore flexibility can enhance permeation properties which will become even more important in future applications to substrate translocation. PMID:27088446
Non-Brownian diffusion in lipid membranes: Experiments and simulations.
Metzler, R; Jeon, J-H; Cherstvy, A G
2016-10-01
The dynamics of constituents and the surface response of cellular membranes-also in connection to the binding of various particles and macromolecules to the membrane-are still a matter of controversy in the membrane biophysics community, particularly with respect to crowded membranes of living biological cells. We here put into perspective recent single particle tracking experiments in the plasma membranes of living cells and supercomputing studies of lipid bilayer model membranes with and without protein crowding. Special emphasis is put on the observation of anomalous, non-Brownian diffusion of both lipid molecules and proteins embedded in the lipid bilayer. While single component, pure lipid bilayers in simulations exhibit only transient anomalous diffusion of lipid molecules on nanosecond time scales, the persistence of anomalous diffusion becomes significantly longer ranged on the addition of disorder-through the addition of cholesterol or proteins-and on passing of the membrane lipids to the gel phase. Concurrently, experiments demonstrate the anomalous diffusion of membrane embedded proteins up to macroscopic time scales in the minute time range. Particular emphasis will be put on the physical character of the anomalous diffusion, in particular, the occurrence of ageing observed in the experiments-the effective diffusivity of the measured particles is a decreasing function of time. Moreover, we present results for the time dependent local scaling exponent of the mean squared displacement of the monitored particles. Recent results finding deviations from the commonly assumed Gaussian diffusion patterns in protein crowded membranes are reported. The properties of the displacement autocorrelation function of the lipid molecules are discussed in the light of their appropriate physical anomalous diffusion models, both for non-crowded and crowded membranes. In the last part of this review we address the upcoming field of membrane distortion by elongated membrane
Differential dynamic microscopy to characterize Brownian motion and bacteria motility
Germain, David; Leocmach, Mathieu; Gibaud, Thomas
2016-03-01
We have developed a lab module for undergraduate students, which involves the process of quantifying the dynamics of a suspension of microscopic particles using Differential Dynamic Microscopy (DDM). DDM is a relatively new technique that constitutes an alternative method to more classical techniques such as dynamic light scattering (DLS) or video particle tracking (VPT). The technique consists of imaging a particle dispersion with a standard light microscope and a camera and analyzing the images using a digital Fourier transform to obtain the intermediate scattering function, an autocorrelation function that characterizes the dynamics of the dispersion. We first illustrate DDM in the textbook case of colloids under Brownian motion, where we measure the diffusion coefficient. Then we show that DDM is a pertinent tool to characterize biological systems such as motile bacteria.
Brownian Dynamics of Colloidal Particles in Lyotropic Chromonic Liquid Crystals
Martinez, Angel; Collings, Peter J.; Yodh, Arjun G.
We employ video microscopy to study the Brownian dynamics of colloidal particles in the nematic phase of lyotropic chromonic liquid crystals (LCLCs). These LCLCs (in this case, DSCG) are water soluble, and their nematic phases are characterized by an unusually large elastic anisotropy. Our preliminary measurements of particle mean-square displacement for polystyrene colloidal particles (~5 micron-diameter) show diffusive and sub-diffusive behaviors moving parallel and perpendicular to the nematic director, respectively. In order to understand these motions, we are developing models that incorporate the relaxation of elastic distortions of the surrounding nematic field. Further experiments to confirm these preliminary results and to determine the origin of these deviations compared to simple diffusion theory are ongoing; our results will also be compared to previous diffusion experiments in nematic liquid crystals. We gratefully acknowledge financial support through NSF DMR12-05463, MRSEC DMR11-20901, and NASA NNX08AO0G.
Mériguet, G; Jardat, M; Turq, P
2004-09-22
We present Brownian dynamics simulations of real charge-stabilized ferrofluids, which are stable colloidal dispersions of magnetic nanoparticles, with and without the presence of an external magnetic field. The colloidal suspensions are treated as collections of monodisperse spherical particles, bearing point dipoles at their centers and undergoing translational and rotational Brownian motions. The overall repulsive isotropic interactions between particles, governed by electrostatic repulsions, are taken into account by a one-component effective pair interaction potential. The potential parameters are fitted in order that computed structure factors are close to the experimental ones. Two samples of ferrofluid differing by the particle diameter and consequently by the intensity of the magnetic interaction are considered here. The magnetization and birefringence curves are computed: a deviation from the ideal Langevin behaviors is observed if the dipolar moment of particles is sufficiently large. Structure factors are also computed from simulations with and without an applied magnetic field H: the microstructure of the repulsive ferrofluid becomes anisotropic under H. Even our simple modeling of the suspension allows us to account for the main experimental features: an increase of the peak intensity is observed in the direction perpendicular to the field whereas the peak intensity decreases in the direction parallel to the field. PMID:15367036
Chung, Shin-Ho; Corry, Ben
2007-01-01
In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to c...
Chen, Shing Bor
2015-12-01
Brownian dynamics simulation has been employed to study the dynamic behavior of particles in three-dimensional ordered porous media subject to a sinusoidal force field. The media comprises interconnected spherical cavities arranged in a simple cubic lattice. The thermal noise assists the particles to undergo cavity hopping, leading to a displacement behavior analogous to stochastic resonance, when the imposed field is strong enough but not aligned with the aperture lines, and the oscillation frequency is not too high. The periodic mean trajectory depends on the strength, frequency, and orientation of the imposed field. At sufficiently large field strength, the periodic particle displacement can become nonsinusoidal due to the strong hindrance and pinning effect of the cavity wall. PMID:26764630
Dubina, Sean Hyun; Wedgewood, Lewis Edward
2016-07-01
Ferrofluids are often favored for their ability to be remotely positioned via external magnetic fields. The behavior of particles in ferromagnetic clusters under uniformly applied magnetic fields has been computationally simulated using the Brownian dynamics, Stokesian dynamics, and Monte Carlo methods. However, few methods have been established that effectively handle the basic principles of magnetic materials, namely, Maxwell's equations. An iterative constraint method was developed to satisfy Maxwell's equations when a uniform magnetic field is imposed on ferrofluids in a heterogeneous Brownian dynamics simulation that examines the impact of ferromagnetic clusters in a mesoscale particle collection. This was accomplished by allowing a particulate system in a simple shear flow to advance by a time step under a uniformly applied magnetic field, then adjusting the ferroparticles via an iterative constraint method applied over sub-volume length scales until Maxwell's equations were satisfied. The resultant ferrofluid model with constraints demonstrates that the magnetoviscosity contribution is not as substantial when compared to homogeneous simulations that assume the material's magnetism is a direct response to the external magnetic field. This was detected across varying intensities of particle-particle interaction, Brownian motion, and shear flow. Ferroparticle aggregation was still extensively present but less so than typically observed.
Dynamics of non-Brownian fiber suspensions under periodic shear.
Franceschini, Alexandre; Filippidi, Emmanouela; Guazzelli, Elisabeth; Pine, David J
2014-09-21
We report experiments studying the dynamics of dense non-Brownian fiber suspensions subjected to periodic oscillatory shear. We find that periodic shear initially causes fibers to collide and to undergo irreversible diffusion. As time progresses, the fibers tend to orient in the vorticity direction while the number of collisions decreases. Ultimately, the system goes to one of two steady states: an absorbing steady state, where collisions cease and the fibers undergo reversible trajectories; an active state, where fibers continue to collide causing them to diffuse and undergo irreversible trajectories. Collisions between fibers can be characterized by an effective volume fraction Φ with a critical volume fraction Φc that separates absorbing from active (diffusing) steady states. The effective volume fraction Φ depends on the mean fiber orientation and thus decreases in time as fibers progressively orient under periodic shear. In the limit that the temporal evolution of Φ is slow compared to the activity relaxation time τ, all the data for all strain amplitudes and all concentrations can be scaled onto a single master curve with a functional dependence well-described by t(-β/ν)R(e(-t)R), where tR is the rescaled time. As Φ → Φc, τ diverges. Therefore, for experiments in which Φ(t) starts above Φc but goes to a steady state below Φc, departures from scaling are observed for Φ very near Φc. The critical exponents are measured to be β = 0.84 ± 0.04 and ν = 1.1 ± 0.1, which is consistent with the Manna universality class for directed percolation. PMID:25068577
Nonlinear Brownian motion - mean square displacement
Directory of Open Access Journals (Sweden)
W.Ebeling
2004-01-01
Full Text Available The stochastic dynamics of self-propelled Brownian particles is studied by means of the Langevin and the Fokker-Planck approach. We model the driving by a nonlinear friction function which has a negative part at small velocities, leading to active Brownian motion of the particles. The mean square displacement is estimated analytically and compared with numerical simulations.
Maldonado-Camargo, L.; Torres-Díaz, I.; Chiu-Lam, A.; Hernández, M.; Rinaldi, C.
2016-08-01
We demonstrate how dynamic magnetic susceptibility measurements (DMS) can be used to estimate the relative contributions of Brownian and Néel relaxation to the dynamic magnetic response of a magnetic fluid, a suspension of magnetic nanoparticles. The method applies to suspensions with particles that respond through Brownian or Néel relaxation and for which the characteristic Brownian and Néel relaxation times are widely separated. First, we illustrate this using magnetic fluids consisting of mixtures of particles that relax solely by the Brownian or Néel mechanisms. Then, it is shown how the same approach can be applied to estimate the relative contributions of Brownian and Néel relaxation in a suspension consisting of particles obtained from a single synthesis and whose size distribution straddles the transition from Néel to Brownian relaxation.
Molecular dynamics test of the Brownian description of Na(+) motion in water
Wilson, M. A.; Pohorille, A.; Pratt, L. R.
1985-01-01
The present paper provides the results of molecular dynamics calculations on a Na(+) ion in aqueous solution. Attention is given to the sodium-oxygen and sodium-hydrogen radial distribution functions, the velocity autocorrelation function for the Na(+) ion, the autocorrelation function of the force on the stationary ion, and the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dyanmics in solution. It is pointed out that the presented calculations provide accurate data for testing theories of ion dynamics in solution. The conducted tests show that it is feasible to calculate Brownian friction constants for ions in aqueous solutions. It is found that for Na(+) under the considered conditions the Brownian mobility is in error by only 60 percent.
Cosseddu, Salvatore M; Allen, Michael P; Rodger, P M; Luchinsky, Dmitry G; McClintock, Peter V E
2013-01-01
The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion's dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.
Cosseddu, S. M.; Khovanov, I. A.; Allen, M. P.; Rodger, P. M.; Luchinsky, D. G.; McClintock, P. V. E.
2013-10-01
The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion's dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.
Khan, Siddique J.
We carry out Brownian Dynamics Simulations to study the self-assembly of ligated gold nanoparticles for various ligand chain lengths. First, we develop a phenomenological model for an effective nanoparticle-nanoparticle pair potential by treating the ligands as flexible polymer chains. Besides van der Waals interactions, we incorporate both the free energy of mixing and elastic contributions from compression of the ligands in our effective pair potentials. The separation of the nanoparticles at the potential minimum compares well with experimental results of gold nanoparticle superlattice constants for various ligand lengths. Next, we use the calculated pair potentials as input to Brownian dynamics simulations for studying the formation of nanoparticle assembly in three dimensions. For dodecanethiol ligated nanoparticles in toluene, our model gives a relatively shallower well depth and the clusters formed after a temperature quench are compact in morphology. Simulation results for the kinetics of cluster growth in this case are compared with phase separations in binary mixtures. For decanethiol ligated nanoparticles, the model well depth is found to be deeper, and simulations show hybrid, fractal-like morphology for the clusters. Cluster morphology in this case shows a compact structure at short length scales and a fractal structure at large length scales. Growth kinetics for this deeper potential depth is compared with the diffusion-limited cluster-cluster aggregation (DLCA) model. We also did simulation studies of nanoparticle supercluster (NPSC) nucleation from a temperature quenched system. Induction periods are observed with times that yield a reasonable supercluster interfacial tension via classical nucleation theory (CNT). However, only the largest pre-nucleating clusters are dense and the cluster size can occasionally range greater than the critical size in the pre-nucleation regime until a cluster with low enough energy occurs, then nucleation ensues. Late
Brownian agents and active particles collective dynamics in the natural and social sciences
Schweitzer, Frank
2007-01-01
""This book lays out a vision for a coherent framework for understanding complex systems"" (from the foreword by J. Doyne Farmer). By developing the genuine idea of Brownian agents, the author combines concepts from informatics, such as multiagent systems, with approaches of statistical many-particle physics. This way, an efficient method for computer simulations of complex systems is developed which is also accessible to analytical investigations and quantitative predictions. The book demonstrates that Brownian agent models can be successfully applied in many different contexts, ranging from
Generalized Scaling and the Master Variable for Brownian Magnetic Nanoparticle Dynamics
Reeves, Daniel B.; Yipeng Shi; Weaver, John B.
2016-01-01
Understanding the dynamics of magnetic particles can help to advance several biomedical nanotechnologies. Previously, scaling relationships have been used in magnetic spectroscopy of nanoparticle Brownian motion (MSB) to measure biologically relevant properties (e.g., temperature, viscosity, bound state) surrounding nanoparticles in vivo. Those scaling relationships can be generalized with the introduction of a master variable found from non-dimensionalizing the dynamical Langevin equation. T...
Brownian Agents and Active Particles: Collective Dynamics in the Natural and Social Sciences
International Nuclear Information System (INIS)
This is a book about the modelling of complex systems and, unlike many books on this subject, concentrates on the discussion of specific systems and gives practical methods for modelling and simulating them. This is not to say that the author does not devote space to the general philosophy and definition of complex systems and agent-based modelling, but the emphasis is definitely on the development of concrete methods for analysing them. This is, in my view, to be welcomed and I thoroughly recommend the book, especially to those with a theoretical physics background who will be very much at home with the language and techniques which are used. The author has developed a formalism for understanding complex systems which is based on the Langevin approach to the study of Brownian motion. This is a mesoscopic description; details of the interactions between the Brownian particle and the molecules of the surrounding fluid are replaced by a randomly fluctuating force. Thus all microscopic detail is replaced by a coarse-grained description which encapsulates the essence of the interactions at the finer level of description. In a similar way, the influences on Brownian agents in a multi-agent system are replaced by stochastic influences which sum up the effects of these interactions on a finer scale. Unlike Brownian particles, Brownian agents are not structureless particles, but instead have some internal states so that, for instance, they may react to changes in the environment or to the presence of other agents. Most of the book is concerned with developing the idea of Brownian agents using the techniques of statistical physics. This development parallels that for Brownian particles in physics, but the author then goes on to apply the technique to problems in biology, economics and the social sciences. This is a clear and well-written book which is a useful addition to the literature on complex systems. It will be interesting to see if the use of Brownian agents becomes
Long-time diffusivity of DNA chains in nanochannels: A Brownian dynamics study
Jain, Aashish; Dorfman, Kevin
2015-03-01
The simplest approach to calculate the diffusivity of any polymer chain is to use the double sum Kirkwood formula, which is based on preaveraging approximation of diffusion tensor. The error due to the preaveraging approximation has been reported by a number of researchers in the context of free solution by computing both Kirkwood diffusivity D (K) (also known as short-time diffusivity) and long-time diffusivity DL. In nanochannels, the main approach to compute the diffusivity is the Kirkwood formula. However, the error due to the preaveraging approximation is not known in a confined system. We use Brownian dynamics simulation algorithm with excluded volume and hydrodynamic interactions to calculate both short-time and long-time diffusivities of DNA chains in nanochannels, and compare them for a range of channel sizes and DNA chain sizes. Our results indicate that the long-time diffusivity is always smaller than the short-time diffusivity, which is consistent with the result obtained in free solution using linear response theory DL
Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions
Bauler, Patricia; Huber, Gary A.; McCammon, J. Andrew
2012-01-01
Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetri...
Application of GPU processing for Brownian particle simulation
Cheng, Way Lee; Sheharyar, Ali; Sadr, Reza; Bouhali, Othmane
2015-01-01
Reports on the anomalous thermal-fluid properties of nanofluids (dilute suspension of nano-particles in a base fluid) have been the subject of attention for 15 years. The underlying physics that govern nanofluid behavior, however, is not fully understood and is a subject of much dispute. The interactions between the suspended particles and the base fluid have been cited as a major contributor to the improvement in heat transfer reported in the literature. Numerical simulations are instrumental in studying the behavior of nanofluids. However, such simulations can be computationally intensive due to the small dimensions and complexity of these problems. In this study, a simplified computational approach for isothermal nanofluid simulations was applied, and simulations were conducted using both conventional CPU and parallel GPU implementations. The GPU implementations significantly improved the computational performance, in terms of the simulation time, by a factor of 1000-2500. The results of this investigation show that, as the computational load increases, the simulation efficiency approaches a constant. At a very high computational load, the amount of improvement may even decrease due to limited system memory.
Differential Dynamic Microscopy to characterize Brownian motion and bacteria motility
Germain, David; Leocmach, Mathieu; Gibaud, Thomas
2015-01-01
We have developed a lab work module where we teach undergraduate students how to quantify the dynamics of a suspension of microscopic particles, measuring and analyzing the motion of those particles at the individual level or as a group. Differential Dynamic Microscopy (DDM) is a relatively recent technique that precisely does that and constitutes an alternative method to more classical techniques such as dynamics light scattering (DLS) or video particle tracking (VPT). DDM consists in imagin...
Energy Technology Data Exchange (ETDEWEB)
Speck, Thomas [Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz (Germany); Menzel, Andreas M.; Bialké, Julian; Löwen, Hartmut [Institut für Theoretische Physik II, Heinrich-Heine-Universität, D-40225 Düsseldorf (Germany)
2015-06-14
Recently, we have derived an effective Cahn-Hilliard equation for the phase separation dynamics of active Brownian particles by performing a weakly non-linear analysis of the effective hydrodynamic equations for density and polarization [Speck et al., Phys. Rev. Lett. 112, 218304 (2014)]. Here, we develop and explore this strategy in more detail and show explicitly how to get to such a large-scale, mean-field description starting from the microscopic dynamics. The effective free energy emerging from this approach has the form of a conventional Ginzburg-Landau function. On the coarsest scale, our results thus agree with the mapping of active phase separation onto that of passive fluids with attractive interactions through a global effective free energy (motility-induced phase transition). Particular attention is paid to the square-gradient term necessary for the phase separation kinetics. We finally discuss results from numerical simulations corroborating the analytical results.
Generalized Langevin Theory Of The Brownian Motion And The Dynamics Of Polymers In Solution
International Nuclear Information System (INIS)
The review deals with a generalization of the Rouse and Zimm bead-spring models of the dynamics of flexible polymers in dilute solutions. As distinct from these popular theories, the memory in the polymer motion is taken into account. The memory naturally arises as a consequence of the fluid and bead inertia within the linearized Navier-Stokes hydrodynamics. We begin with a generalization of the classical theory of the Brownian motion, which forms the basis of any theory of the polymer dynamics. The random force driving the Brownian particles is not the white one as in the Langevin theory, but “colored”, i.e., statistically correlated in time, and the friction force on the particles depends on the history of their motion. An efficient method of solving the resulting generalized Langevin equations is presented and applied to the solution of the equations of motion of polymer beads. The memory effects lead to several peculiarities in the time correlation functions used to describe the dynamics of polymer chains. So, the mean square displacement of the polymer coils contains algebraic long-time tails and at short times it is ballistic. It is shown how these features reveal in the experimentally observable quantities, such as the dynamic structure factors of the scattering or the viscosity of polymer solutions. A phenomenological theory is also presented that describes the dependence of these quantities on the polymer concentration in solution. (author)
A Brownian motion technique to simulate gasification and its application to C/C composite ablation
International Nuclear Information System (INIS)
Ablation of carbon-carbon composites (C/C) results in a heterogeneous surface recession mainly due to some gasification processes (oxidation, sublimation) possibly coupled to bulk mass transfer. In order to simulate and analyse the material/environment interactions during ablation, a Brownian motion simulation method featuring special Random Walk rules close to the wall has been implemented to efficiently simulate mass transfer in the low Peclet number regime. A sticking probability law adapted to this kind of Random Walk has been obtained for first-order heterogeneous reactions. In order to simulate the onset of surface roughness, the interface recession is simultaneously handled in 3D using a Simplified Marching Cube discretization. This tool is validated by comparison to analytical models. Then, its ability to provide reliable and accurate solutions of ablation phenomena in 3D is illustrated. (authors)
Generalized Scaling and the Master Variable for Brownian Magnetic Nanoparticle Dynamics
Reeves, Daniel B.; Shi, Yipeng; Weaver, John B.
2016-01-01
Understanding the dynamics of magnetic particles can help to advance several biomedical nanotechnologies. Previously, scaling relationships have been used in magnetic spectroscopy of nanoparticle Brownian motion (MSB) to measure biologically relevant properties (e.g., temperature, viscosity, bound state) surrounding nanoparticles in vivo. Those scaling relationships can be generalized with the introduction of a master variable found from non-dimensionalizing the dynamical Langevin equation. The variable encapsulates the dynamical variables of the surroundings and additionally includes the particles’ size distribution and moment and the applied field’s amplitude and frequency. From an applied perspective, the master variable allows tuning to an optimal MSB biosensing sensitivity range by manipulating both frequency and field amplitude. Calculation of magnetization harmonics in an oscillating applied field is also possible with an approximate closed-form solution in terms of the master variable and a single free parameter. PMID:26959493
Chernov, N.; Dolgopyat, D.
2008-01-01
A classical model of Brownian motion consists of a heavy molecule submerged into a gas of light atoms in a closed container. In this work we study a 2D version of this model, where the molecule is a heavy disk of mass M and the gas is represented by just one point particle of mass m = 1, which interacts with the disk and the walls of the container via elastic collisions. Chaotic behavior of the particles is ensured by convex (scattering) walls of the container. We prove that the position and ...
Shit, Anindita; Chattopadhyay, Sudip; Chaudhuri, Jyotipratim Ray
2011-06-01
We explore the Brownian dynamics in the quantum regime (by investigating the quantum Langevin and Smoluchowski equations) in terms of an effective time-independent Hamiltonian in the presence of a rapidly oscillating field. We achieve this by systematically expanding the time-dependent system-reservoir Hamiltonian in the inverse of driving frequency with a systematic time-scale separation and invoking a quantum gauge transformation within the framework of Floquet theorem. PMID:21797289
Elamin, Khalid; Swenson, Jan
2015-03-01
Aqueous solutions of glycerol are investigated by dynamic light scattering (DLS) over the whole concentration range (10-98 wt.% water) and in the temperature range 283-303 K. The measurements reveal one slow relaxation process in the geometry of polarized light scattering. This process is present in the whole concentration range, although it is very weak at the highest and lowest water concentrations and is considerably slower than the structural α relaxation, which is too fast to be observed on the experimental time scale in the measured temperature range. The relaxation time of the observed process exhibits a 1/q2 dependence, proving that it is due to long-range translational diffusion. The Stokes-Einstein relation is used to estimate the hydrodynamic radius of the diffusing particles and from these calculations it is evident that the observed relaxation process is due to the Brownian motion of single or a few glycerol molecules. The fact that it is possible to study the self-diffusion of such small molecules may stimulate a broadening of the research field used to be covered by the DLS technique. PMID:25871109
Chavanis, Pierre-Henri; Sire, Clément
2006-06-01
We propose a general kinetic and hydrodynamic description of self-gravitating Brownian particles in d dimensions. We go beyond the usual approximations by considering inertial effects and finite-N effects while previous works use a mean-field approximation valid in a proper thermodynamic limit (N --> +infinity) and consider an overdamped regime (xi --> +infinity). We recover known models in some particular cases of our general description. We derive the expression of the virial theorem for self-gravitating Brownian particles and study the linear dynamical stability of isolated clusters of particles and uniform systems by using techniques introduced in astrophysics. We investigate the influence of the equation of state, of the dimension of space, and of the friction coefficient on the dynamical stability of the system. We obtain the exact expression of the critical temperature Tc for a multicomponents self-gravitating Brownian gas in d = 2. We also consider the limit of weak frictions, xi --> 0, and derive the orbit-averaged Kramers equation. PMID:16906911
Brownian Dynamics of a Suspension of Particles with Constrained Voronoi Cell Volumes
Singh, John P.
2015-06-23
© 2015 American Chemical Society. Solvent-free polymer-grafted nanoparticle fluids consist of inorganic core particles fluidized by polymers tethered to their surfaces. The attachment of the suspending fluid to the particle surface creates a strong penalty for local variations in the fluid volume surrounding the particles. As a model of such a suspension we perform Brownian dynamics of an equilibrium system consisting of hard spheres which experience a many-particle potential proportional to the variance of the Voronoi volumes surrounding each particle (E = α(V
De Biase, Pablo M; Markosyan, Suren; Noskov, Sergei
2015-02-01
The transport of ions and solutes by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. The time scale involved in the polymer transport across a nanopore is beyond the accessibility of conventional MD simulations. Moreover, experimental studies lack sufficient resolution to provide details on the molecular underpinning of the transport mechanisms. BROMOC, the code presented herein, performs Brownian dynamics simulations, both serial and parallel, up to several milliseconds long. BROMOC can be used to model large biological systems. IMC-MACRO software allows for the development of effective potentials for solute-ion interactions based on radial distribution function from all-atom MD. BROMOC Suite also provides a versatile set of tools to do a wide variety of preprocessing and postsimulation analysis. We illustrate a potential application with ion and ssDNA transport in MspA nanopore. PMID:25503688
Millen, J; Deesuwan, T; Barker, P; Anders, J
2014-06-01
Einstein realized that the fluctuations of a Brownian particle can be used to ascertain the properties of its environment. A large number of experiments have since exploited the Brownian motion of colloidal particles for studies of dissipative processes, providing insight into soft matter physics and leading to applications from energy harvesting to medical imaging. Here, we use heated optically levitated nanospheres to investigate the non-equilibrium properties of the gas surrounding them. Analysing the sphere's Brownian motion allows us to determine the temperature of the centre-of-mass motion of the sphere, its surface temperature and the heated gas temperature in two spatial dimensions. We observe asymmetric heating of the sphere and gas, with temperatures reaching the melting point of the material. This method offers opportunities for accurate temperature measurements with spatial resolution on the nanoscale, and provides a means for testing non-equilibrium thermodynamics. PMID:24793558
Mezzasalma, Stefano A
2007-03-15
The theoretical basis of a recent theory of Brownian relativity for polymer solutions is deepened and reexamined. After the problem of relative diffusion in polymer solutions is addressed, its two postulates are formulated in all generality. The former builds a statistical equivalence between (uncorrelated) timelike and shapelike reference frames, that is, among dynamical trajectories of liquid molecules and static configurations of polymer chains. The latter defines the "diffusive horizon" as the invariant quantity to work with in the special version of the theory. Particularly, the concept of universality in polymer physics corresponds in Brownian relativity to that of covariance in the Einstein formulation. Here, a "universal" law consists of a privileged observation, performed from the laboratory rest frame and agreeing with any diffusive reference system. From the joint lack of covariance and simultaneity implied by the Brownian Lorentz-Poincaré transforms, a relative uncertainty arises, in a certain analogy with quantum mechanics. It is driven by the difference between local diffusion coefficients in the liquid solution. The same transformation class can be used to infer Fick's second law of diffusion, playing here the role of a gauge invariance preserving covariance of the spacetime increments. An overall, noteworthy conclusion emerging from this view concerns the statistics of (i) static macromolecular configurations and (ii) the motion of liquid molecules, which would be much more related than expected. PMID:17223124
Quantal Brownian Motion from RPA dynamics: The master and Fokker-Planck equations
International Nuclear Information System (INIS)
From the purely quantal RPA description of the damped harmonic oscillator and of the corresponding Brownian Motion within the full space (phonon subspace plus reservoir), a master equation (as well as a Fokker-Planck equation) for the reduced density matrix (for the reduced Wigner function, respectively) within the phonon subspace is extracted. The RPA master equation agrees with the master equation derived by the time-dependent perturbative approaches which utilize Tamm-Dancoff Hilbert spaces and invoke the rotating wave approximation. Since the RPA yields a full, as well as a contracted description, it can account for both the kinetic and the unperturbed oscillator momenta. The RPA description of the quantal Brownian Motion contrasts with the descriptions provided by the time perturbative approaches whether they invoke or not the rotating wave approximation. The RPA description also contrasts with the phenomenological phase space quantization. (orig.)
Dynamics of 2D Stochastic non-Newtonian fluids driven by fractional Brownian motion
Li, Jin; Huang, Jianhua
2011-01-01
A 2D Stochastic incompressible non-Newtonian fluids driven by fractional Bronwnian motion with Hurst parameter $H \\in (1/2,1)$ is studied. The Wiener-type stochastic integrals are introduced for infinite-dimensional fractional Brownian motion. Four groups of assumptions, including the requirement of Nuclear operator or Hilbert-Schmidt operator, are discussed. The existence and regularity of stochastic convolution for the corresponding additive linear stochastic equation are obtained under eac...
Chavanis, Pierre-Henri; Sire, Clément
2006-06-01
We derive the virial theorem appropriate to the generalized Smoluchowski-Poisson (GSP) system describing self-gravitating Brownian particles in an overdamped limit. We extend previous works by considering the case of an unbounded domain and an arbitrary equation of state. We use the virial theorem to study the diffusion (evaporation) of an isothermal Brownian gas above the critical temperature Tc in dimension d = 2 and show how the effective diffusion coefficient and the Einstein relation are modified by self-gravity. We also study the collapse at T = Tc and show that the central density increases logarithmically with time instead of exponentially in a bounded domain. Finally, for d > 2, we show that the evaporation of the system is essentially a pure diffusion slightly slowed down by self-gravity. We also study the linear dynamical stability of stationary solutions of the GSP system representing isolated clusters of particles and investigate the influence of the equation of state and of the dimension of space on the dynamical stability of the system. PMID:16906910
Lu, Zhumin; Dou, Hua-Shu; Phan-Thien, Nhan; Yeo, Khoon Seng
2008-01-01
In this paper, the finite element method is combined with the Brownian Configuration Field (BFC) method to simulate the fibre suspension flow in axisymmetric contraction and expansion passages. In order to solve for the high stress at high concentration, the Discrete Adaptive Viscoelastic Stress Splitting (DAVSS) method is employed. For the axisymmetric contraction and expansion passages with different geometry ratios, the results obtained are compared to available constitutive models and experiments. The predicted vortex length for dilute suspensions agrees well with experimental data in literature. Our numerical results show clearly the effect on vortex enhancement with increase of the volume fractions and the aspect ratios. Effect of aspect ratio of fibres on the vortex length is also studied. It is found that for the lower expansion ratio flows the vortex dimension in the corner region is fairly independent of fibre concentration and aspect ratio of fibres while the said vortex dimension increases with th...
Directory of Open Access Journals (Sweden)
Ryo Kanada
Full Text Available Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."
Dynamics simulations for engineering macromolecular interactions
Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey
2013-06-01
The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could
Stokesian Dynamic Simulations of Colloid Assembly at a Fluid Interface
Dani, Archit; Maldarelli, Charles
2015-11-01
The collective dynamics and self-assembly of colloids floating at a gas/liquid or a liquid/liquid interface is a balance between deterministic lateral interaction forces, e.g. capillary attraction and dipolar electrostatic repulsion if the particles are charged, viscous resistance to colloid motion along the surface and thermal fluctuations. As the colloid size decreases, thermal (Brownian) forces become important and can affect the self assembly into ordered patterns and crystal structures that are the starting point for materials applications. Stokesian dynamics simulations are presented to describe the lateral organization of particles along the surface in Brownian dominated regimes that includes (using a pairwise approximation) capillary attraction and the hydrodynamic interaction between particles (incorporating the effect of the particle immersion depth) and thermal fluctuations. Clustering, fractal growth and particle ordering are observed at critically large values of the Peclet numbers, while smaller values yield states in which particles remain uncorrelated in space and more widely separated.
Role of Brownian motion on the thermal conductivity enhancement of nanofluids
Gupta, Amit; Kumar, Ranganathan
2007-11-01
This study involves Brownian dynamics simulations of a real nanofluid system in which the interparticle potential is determined based on Debye length and surface interaction of the fluid and the solid. This paper shows that Brownian motion can increase the thermal conductivity of the nanofluid by 6% primarily due to "random walk" motion and not only through diffusion. This increase is limited by the maximum concentration for each particle size and is below that predicted by the effective medium theory. Beyond the maximum limit, particle aggregates begin to form. Brownian motion contribution stays as a constant beyond a certain particle diameter.
Gomez-Marin, A.; Sancho, J. M.
2004-01-01
In this paper we present a model of a symmetric Brownian motor (SBM) which changes the sign of its velocity when the temperature gradient is inverted. The velocity, external work and efficiency are studied as a function of the temperatures of the baths and other relevant parameters. The motor shows a current reversal when another parameter (a phase shift) is varied. Analytical predictions and results from numerical simulations are performed and agree very well. Generic properties of this type...
Institute of Scientific and Technical Information of China (English)
Jian-Zhong Lin; Fu-Jun Gan
2012-01-01
The Brownian coagulation of nanoparticles with initial bimodal size distribution,i.e.,mode i and j,is numerically studied using the moment method.Evolutions of particle number concentration,geometric average diameter and geometric standard deviation are given in the free molecular regime,the continuum regime,the free molecular regimand transition regime,the free molecular regime and contin-uum regime,respectively.The results show that,both in the free molecular regime and the continuum regime,the number concentration of mode i and j decreases with increasing time.The evolutions of particle geometric average diameter with different initial size distribution are quite different.Both intra-modal and inter-modal coagulation finally make the polydispersed size distribution become monodispersed.As time goes by,the size distribution with initial bimodal turns to be unimodal and shifts to a larger particle size range.In the free molecular regime and transition regime,the intermodal coagulation becomes dominant when the number concentrations of mode i and j are of the same order.The effects of the number concentration of mode i and mode j on the evolution of geometric average diameter of mode j are negligible,while the effects of the number concentration of mode j on the evolution of geometric average diameter of mode j is distinct.In the free molecular regime and continuum regime,the higher the initial number concentration of mode j,the more obvious the variation of the number concentration of mode i.
Effect of interfaces on the nearby Brownian motion
Huang, Kai
2016-01-01
Near-boundary Brownian motion is a classic hydrodynamic problem of great importance in a variety of fields, from biophysics to micro-/nanofluidics. However, due to challenges in experimental measurements of near-boundary dynamics, the effect of interfaces on Brownian motion has remained elusive. Here, we report a computational study of this effect using microsecond-long large-scale molecular dynamics simulations and our newly developed Green-Kubo relation for friction at the liquid-solid interface. Our computer experiment unambiguously reveals that the t^(-3/2) long-time decay of the velocity autocorrelation function of a Brownian particle in bulk liquid is replaced by a t^(-5/2) decay near a boundary. We discover a general breakdown of traditional no-slip boundary condition at short time scales and we show that this breakdown has a profound impact on the near-boundary Brownian motion. Our results demonstrate the potential of Brownian-particle based micro-/nano-sonar to probe the local wettability of liquid-s...
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Interactive Dynamic-System Simulation
Korn, Granino A
2010-01-01
Showing you how to use personal computers for modeling and simulation, Interactive Dynamic-System Simulation, Second Edition provides a practical tutorial on interactive dynamic-system modeling and simulation. It discusses how to effectively simulate dynamical systems, such as aerospace vehicles, power plants, chemical processes, control systems, and physiological systems. Written by a pioneer in simulation, the book introduces dynamic-system models and explains how software for solving differential equations works. After demonstrating real simulation programs with simple examples, the author
Chavanis, Pierre-Henri; Sire, Clement
2005-01-01
We derive the Virial theorem appropriate to the generalized Smoluchowski-Poisson system describing self-gravitating Brownian particles and bacterial populations (chemotaxis). We extend previous works by considering the case of an unbounded domain and an arbitrary equation of state. We use the Virial theorem to study the diffusion (evaporation) of an isothermal Brownian gas above the critical temperature T_c in dimension d=2 and show how the effective diffusion coefficient and the Einstein rel...
Interacting Brownian Swarms: Some Analytical Results
Directory of Open Access Journals (Sweden)
Guillaume Sartoretti
2016-01-01
Full Text Available We consider the dynamics of swarms of scalar Brownian agents subject to local imitation mechanisms implemented using mutual rank-based interactions. For appropriate values of the underlying control parameters, the swarm propagates tightly and the distances separating successive agents are iid exponential random variables. Implicitly, the implementation of rank-based mutual interactions, requires that agents have infinite interaction ranges. Using the probabilistic size of the swarm’s support, we analytically estimate the critical interaction range below that flocked swarms cannot survive. In the second part of the paper, we consider the interactions between two flocked swarms of Brownian agents with finite interaction ranges. Both swarms travel with different barycentric velocities, and agents from both swarms indifferently interact with each other. For appropriate initial configurations, both swarms eventually collide (i.e., all agents interact. Depending on the values of the control parameters, one of the following patterns emerges after collision: (i Both swarms remain essentially flocked, or (ii the swarms become ultimately quasi-free and recover their nominal barycentric speeds. We derive a set of analytical flocking conditions based on the generalized rank-based Brownian motion. An extensive set of numerical simulations corroborates our analytical findings.
Wu, Xiaobin; Qiu, Jian; Luo, Kaiqing; Han, Peng
2015-08-01
Dynamic Light Scattering is used for measuring particle size distribution of nano-particle under Brownian motion. Signal is detected through a photomultiplier and processed by correlation analysis, and results are inverted at last. Method by using CCD camera can record the procedure of motion. However, there are several weaknesses such as low refresh speed and noise from CCD camera, and this method depends on particle size and detecting angle. A simulation of nano-particle under Brownian motion is proposed to record dynamic images, studies contrast of dynamic images which can represent speed of diffusion, and its characteristic under different conditions. The results show that through contrast of dynamic images diffusion coefficient can be obtained, which is independent on density of scattering volume.
Molecular dynamics simulations
International Nuclear Information System (INIS)
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs
Blending Brownian motion and heat equation
Cristiani, Emiliano
2015-01-01
In this short communication we present an original way to couple the Brownian motion and the heat equation. More in general, we suggest a way for coupling the Langevin equation for a particle, which describes a single realization of its trajectory, with the associated Fokker-Planck equation, which instead describes the evolution of the particle's probability density function. Numerical results show that it is indeed possible to obtain a regularized Brownian motion and a Brownianized heat equation still preserving the global statistical properties of the solutions. The results also suggest that the more macroscale leads the dynamics the more one can reduce the microscopic degrees of freedom.
Canonical active Brownian motion
Gluck, Alexander; Huffel, Helmuth; Ilijic, Sasa
2008-01-01
Active Brownian motion is the complex motion of active Brownian particles. They are active in the sense that they can transform their internal energy into energy of motion and thus create complex motion patterns. Theories of active Brownian motion so far imposed couplings between the internal energy and the kinetic energy of the system. We investigate how this idea can be naturally taken further to include also couplings to the potential energy, which finally leads to a general theory of cano...
A multiscale guide to Brownian motion
Grebenkov, Denis S.; Belyaev, Dmitry; Jones, Peter W.
2016-01-01
We revise the Lévy construction of Brownian motion as a simple though rigorous approach to operate with various Gaussian processes. A Brownian path is explicitly constructed as a linear combination of wavelet-based ‘geometrical features’ at multiple length scales with random weights. Such a wavelet representation gives a closed formula mapping of the unit interval onto the functional space of Brownian paths. This formula elucidates many classical results about Brownian motion (e.g., non-differentiability of its path), providing an intuitive feeling for non-mathematicians. The illustrative character of the wavelet representation, along with the simple structure of the underlying probability space, is different from the usual presentation of most classical textbooks. Similar concepts are discussed for the Brownian bridge, fractional Brownian motion, the Ornstein-Uhlenbeck process, Gaussian free fields, and fractional Gaussian fields. Wavelet representations and dyadic decompositions form the basis of many highly efficient numerical methods to simulate Gaussian processes and fields, including Brownian motion and other diffusive processes in confining domains.
A dynamic mesh refinement technique for Lattice Boltzmann simulations on octree-like grids
Neumann, Philipp
2012-04-27
In this contribution, we present our new adaptive Lattice Boltzmann implementation within the Peano framework, with special focus on nanoscale particle transport problems. With the continuum hypothesis not holding anymore on these small scales, new physical effects - such as Brownian fluctuations - need to be incorporated. We explain the overall layout of the application, including memory layout and access, and shortly review the adaptive algorithm. The scheme is validated by different benchmark computations in two and three dimensions. An extension to dynamically changing grids and a spatially adaptive approach to fluctuating hydrodynamics, allowing for the thermalisation of the fluid in particular regions of interest, is proposed. Both dynamic adaptivity and adaptive fluctuating hydrodynamics are validated separately in simulations of particle transport problems. The application of this scheme to an oscillating particle in a nanopore illustrates the importance of Brownian fluctuations in such setups. © 2012 Springer-Verlag.
Cooperative Transport of Brownian Particles
Derenyi, Imre; Vicsek, Tamas
1998-01-01
We consider the collective motion of finite-sized, overdamped Brownian particles (e.g., motor proteins) in a periodic potential. Simulations of our model have revealed a number of novel cooperative transport phenomena, including (i) the reversal of direction of the net current as the particle density is increased and (ii) a very strong and complex dependence of the average velocity on both the size and the average distance of the particles.
Popov, Ivan; Vitkin, Alex
2016-01-01
The study of flowing Brownian particles finds numerous biomedical applications, ranging from blood flow analysis to diffusion research. A mathematical model for the correlation function of laser radiation scattered by flowing Brownian particles measured with fiber-based optical coherence tomography (OCT), which accounts for the effects of sample arm optics, is presented. It is shown that the parameters of an OCT optical system of any complexity can be taken into account by using the ABCD ray tracing matrix approach. Specifically, the impact of any optical system can be characterized by the changes in the effective beam radius, which replaces the Gaussian beam radius in the existing mathematical models of scattered radiation. It is shown that the validity of the developed ABCD matrix formalism is governed by the condition that the source coherence length is much smaller than the Rayleigh range in the sample. The predictions of the developed model are compared with previously published theories and with experimental data and agree well with the latter.
Lawler, Gregory F.; Werner, Wendelin
2003-01-01
We define a natural conformally invariant measure on unrooted Brownian loops in the plane and study some of its properties. We relate this measure to a measure on loops rooted at a boundary point of a domain and show how this relation gives a way to ``chronologically add Brownian loops'' to simple curves in the plane.
Radiation Reaction on Brownian Motions
Seto, Keita
2016-01-01
Tracking the real trajectory of a quantum particle is one of the interpretation problem and it is expressed by the Brownian (stochastic) motion suggested by E. Nelson. Especially the dynamics of a radiating electron, namely, radiation reaction which requires us to track its trajectory becomes important in the high-intensity physics by PW-class lasers at present. It has been normally treated by the Furry picture in non-linear QED, but it is difficult to draw the real trajectory of a quantum particle. For the improvement of this, I propose the representation of a stochastic particle interacting with fields and show the way to describe radiation reaction on its Brownian motion.
Shen, Meng; Lueptow, Richard M
2016-01-01
The Angstrom-scale transport characteristics of water and six different solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polyamide reverse osmosis (RO) membrane, FT-30, using non-equilibrium molecular dynamics (NEMD) simulations. Results indicate that water transport increases with an increasing fraction of connected percolated free volume, or water-accessible open space, in the membrane polymer structure. This free volume is enhanced by the dynamic structure of the membrane at the molecular level as it swells when hydrated and vibrates due to molecular collisions allowing a continuous path connecting the opposite membrane surfaces. The tortuous paths available for transport of solutes result in Brownian motion of solute molecules and hopping from pore to pore as they pass through the polymer network structure of the membrane. The transport of alcohol solutes decreases for solutes with larger Van der Waals volume, which corresponds to less available percolated free volume, or sol...
Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer
Directory of Open Access Journals (Sweden)
Casuyac Miqueas
2016-01-01
Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Quantum trajectories for Brownian motion
Strunz, W T; Gisin, Nicolas; Yu, T; Strunz, Walter T.; Diosi, Lajos; Gisin, Nicolas
1999-01-01
We present the stochastic Schroedinger equation for the dynamics of a quantum particle coupled to a high temperature environment and apply it the dynamics of a driven, damped, nonlinear quantum oscillator. Apart from an initial slip on the environmental memory time scale, in the mean, our result recovers the solution of the known non-Lindblad quantum Brownian motion master equation. A remarkable feature of our approach is its localization property: individual quantum trajectories remain localized wave packets for all times, even for the classically chaotic system considered here, the localization being stronger the smaller $\\hbar$.
Brownian Motion in Minkowski Space
Directory of Open Access Journals (Sweden)
Paul O'Hara
2015-06-01
Full Text Available We construct a model of Brownian motion in Minkowski space. There are two aspects of the problem. The first is to define a sequence of stopping times associated with the Brownian “kicks” or impulses. The second is to define the dynamics of the particle along geodesics in between the Brownian kicks. When these two aspects are taken together, the Central Limit Theorem (CLT leads to temperature dependent four dimensional distributions defined on Minkowski space, for distances and 4-velocities. In particular, our processes are characterized by two independent time variables defined with respect to the laboratory frame: a discrete one corresponding to the stopping times when the impulses take place and a continuous one corresponding to the geodesic motion in-between impulses. The subsequent distributions are solutions of a (covariant pseudo-diffusion equation which involves derivatives with respect to both time variables, rather than solutions of the telegraph equation which has a single time variable. This approach simplifies some of the known problems in this context.
Role of Brownian Motion Hydrodynamics on Nanofluid Thermal Conductivity
Energy Technology Data Exchange (ETDEWEB)
W Evans, J Fish, P Keblinski
2005-11-14
We use a simple kinetic theory based analysis of heat flow in fluid suspensions of solid nanoparticles (nanofluids) to demonstrate that the hydrodynamics effects associated with Brownian motion have a minor effect on the thermal conductivity of the nanofluid. Our conjecture is supported by the results of molecular dynamics simulations of heat flow in a model nanofluid with well-dispersed particles. Our findings are consistent with the predictions of the effective medium theory as well as with recent experimental results on well dispersed metal nanoparticle suspensions.
Coupling of lever arm swing and biased Brownian motion in actomyosin.
Directory of Open Access Journals (Sweden)
Qing-Miao Nie
2014-04-01
Full Text Available An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement. In this study, we address the long-standing controversy between the lever-arm hypothesis and the Brownian motion hypothesis through in silico observations of an actomyosin system. We study a system composed of myosin II and actin filament by calculating free-energy landscapes of actin-myosin interactions using the molecular dynamics method and by simulating transitions among dynamically changing free-energy landscapes using the Monte Carlo method. The results obtained by this combined multi-scale calculation show that myosin with inorganic phosphate (Pi and ADP weakly binds to actin and that after releasing Pi and ADP, myosin moves along the actin filament toward the strong-binding site by exhibiting the biased Brownian motion, a behavior consistent with the observed single-molecular behavior of myosin. Conformational flexibility of loops at the actin-interface of myosin and the N-terminus of actin subunit is necessary for the distinct bias in the Brownian motion. Both the 5.5-11 nm displacement due to the biased Brownian motion and the 3-5 nm displacement due to lever-arm swing contribute to the net displacement of myosin. The calculated results further suggest that the recovery stroke of the lever arm plays an important role in enhancing the displacement of myosin through multiple cycles of ATP hydrolysis, suggesting a unified movement mechanism for various members of the myosin family.
Simulations with dynamical HISQ quarks
Bazavov, A; DeTar, C; Freeman, W; Gottlieb, Steven; Heller, U M; Hetrick, J E; Laiho, J; Levkova, L; Oktay, M; Osborn, J; Sugar, R L; Toussaint, D; Van de Water, R S
2010-01-01
We report on the status of a program of generating and using configurations with four flavors of dynamical quarks, using the HISQ action. We study the lattice spacing dependence of physical quantities in these simulations, using runs at several lattice spacings, but with the light quark mass held fixed at two tenths of the strange quark mass. We find that the lattice artifacts in the HISQ simulations are much smaller than those in the asqtad simulations at the same lattice spacings and quark masses. We also discuss methods for setting the scale, or assigning a lattice spacing to ensembles run at unphysical parameters.
International Nuclear Information System (INIS)
The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R1, R2 and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, however, the long chain of dependencies required for its calculation complicates the model-free chi-squared space. Convolutions are induced by the Lorentzian form of the spectral density functions, the linear recombinations of certain spectral density values to obtain the relaxation rates, the calculation of the NOE using the ratio of two of these rates, and finally the quadratic form of the chi-squared equation itself. Two major topological features of the model-free space complicate optimisation. The first is a long, shallow valley which commences at infinite correlation times and gradually approaches the minimum. The most severe convolution occurs for motions on two timescales in which the minimum is often located at the end of a long, deep, curved tunnel or multidimensional valley through the space. A large number of optimisation algorithms will be investigated and their performance compared to determine which techniques are suitable for use in model-free analysis. Local optimisation algorithms will be shown to be sufficient for minimisation not only within the model-free space but also for the minimisation of the Brownian rotational diffusion tensor. In addition the performance of the programs Modelfree and Dasha are investigated. A number of model-free optimisation failures were identified: the inability to slide along the limits, the singular matrix failure of the Levenberg-Marquardt minimisation algorithm, the low precision of both programs, and a bug in Modelfree. Significantly, the singular matrix failure of the Levenberg-Marquardt algorithm occurs when internal correlation times are undefined and is greatly amplified in model-free analysis by both
Brownian particles in supramolecular polymer solutions
Gucht, van der J.; Besseling, N.A.M.; Knoben, W.; Bouteiller, L.; Cohen Stuart, M.A.
2003-01-01
The Brownian motion of colloidal particles embedded in solutions of hydrogen-bonded supramolecular polymers has been studied using dynamic light scattering. At short times, the motion of the probe particles is diffusive with a diffusion coefficient equal to that in pure solvent. At intermediate time
An efficient dissipative particle dynamics-based algorithm for simulating electrolyte solutions
Medina, Stefan; Wang, Zhen-Gang; Schmid, Friederike
2014-01-01
We propose an efficient simulation algorithm based on the dissipative particle dynamics (DPD) method for studying electrohydrodynamic phenomena in electrolyte fluids. The fluid flow is mimicked with DPD particles while the evolution of the concentration of the ionic species is described using Brownian pseudo particles. The method is designed especially for systems with high salt concentrations, as explicit treatment of the salt ions becomes computationally expensive. For illustration, we apply the method to electro-osmotic flow over patterned, superhydrophobic surfaces. The results are in good agreement with recent theoretical predictions.
Vehicle dynamics modeling and simulation
Schramm, Dieter; Bardini, Roberto
2014-01-01
The authors examine in detail the fundamentals and mathematical descriptions of the dynamics of automobiles. In this context different levels of complexity will be presented, starting with basic single-track models up to complex three-dimensional multi-body models. A particular focus is on the process of establishing mathematical models on the basis of real cars and the validation of simulation results. The methods presented are explained in detail by means of selected application scenarios.
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Dynamic simulations of tissue welding
Energy Technology Data Exchange (ETDEWEB)
Maitland, D.J.; Eder, D.C.; London, R.A.; Glinsky, M.E. [and others
1996-02-01
The exposure of human skin to near-infrared radiation is numerically simulated using coupled laser, thermal transport and mass transport numerical models. The computer model LATIS is applied in both one-dimensional and two-dimensional geometries. Zones within the skin model are comprised of a topical solder, epidermis, dermis, and fatty tissue. Each skin zone is assigned initial optical, thermal and water density properties consistent with values listed in the literature. The optical properties of each zone (i.e. scattering, absorption and anisotropy coefficients) are modeled as a kinetic function of the temperature. Finally, the water content in each zone is computed from water diffusion where water losses are accounted for by evaporative losses at the air-solder interface. The simulation results show that the inclusion of water transport and evaporative losses in the model are necessary to match experimental observations. Dynamic temperature and damage distributions are presented for the skin simulations.
Atzberger, P. J.
2007-01-01
In this paper a direct correspondence is made between the effective stochastic dynamics of elastic structures of an Immersed Boundary Method incorporating thermal fluctuations and Stokesian-Browman Dynamics. The correspondence is made in the limit of small Reynolds number, in which the fluid relaxes rapidly on the time scale of the motion of the immersed structures, by performing an averaging procedure directly on the stochastic equations of the Immersed Boundary Method. It is found that the...
Noncommutative Brownian motion
Santos, Willien O; Souza, Andre M C
2016-01-01
We investigate the Brownian motion of a particle in a two-dimensional noncommutative (NC) space. Using the standard NC algebra embodied by the sympletic Weyl-Moyal formalism we find that noncommutativity induces a non-vanishing correlation between both coordinates at different times. The effect itself stands as a signature of spatial noncommutativity and offers further alternatives to experimentally detect the phenomena.
Meurs, P.; Broeck, C. Van Den
2005-01-01
Recently, a thermal Brownian motor was introduced [Van den Broeck, Kawai and Meurs, Phys. Rev. Lett. (2004)], for which an exact microscopic analysis is possible. The purpose of this paper is to review some further properties of this construction, and to discuss in particular specific issues including the relation with macroscopic response and the efficiency at maximum power.
International Nuclear Information System (INIS)
Finding the dynamics of an entire macromolecule is a complex problem as the model-free parameter values are intricately linked to the Brownian rotational diffusion of the molecule, mathematically through the autocorrelation function of the motion and statistically through model selection. The solution to this problem was formulated using set theory as an element of the universal set U-the union of all model-free spaces (d'Auvergne EJ and Gooley PR (2007) Mol BioSyst 3(7), 483-494). The current procedure commonly used to find the universal solution is to initially estimate the diffusion tensor parameters, to optimise the model-free parameters of numerous models, and then to choose the best model via model selection. The global model is then optimised and the procedure repeated until convergence. In this paper a new methodology is presented which takes a different approach to this diffusion seeded model-free paradigm. Rather than starting with the diffusion tensor this iterative protocol begins by optimising the model-free parameters in the absence of any global model parameters, selecting between all the model-free models, and finally optimising the diffusion tensor. The new model-free optimisation protocol will be validated using synthetic data from Schurr JM et al. (1994) J Magn Reson B 105(3), 211-224 and the relaxation data of the bacteriorhodopsin (1-36)BR fragment from Orekhov VY (1999) J Biomol NMR 14(4), 345-356. To demonstrate the importance of this new procedure the NMR relaxation data of the Olfactory Marker Protein (OMP) of Gitti R et al. (2005) Biochem 44(28), 9673-9679 is reanalysed. The result is that the dynamics for certain secondary structural elements is very different from those originally reported
Directory of Open Access Journals (Sweden)
Wenzheng Cui
2015-09-01
Full Text Available Nanofluids are a new generation of high-efficiency refrigerant with abnormal increased thermal conductivity and convective heat transfer properties. In view of the paucity of research work on the contribution of nanoparticle Brownian motion for the thermal conductivity augmentation, the present paper carries out a series of MD simulations to explorer the order of magnitude of nanoparticle Brownian motion and discusses the effect of nanoparticle Brownian motion for thermal conductivity enhancement of nanofluids. Various influence factors including nanoparticle shapes, sizes, and materials are considered. The Brownian motion of nanoparticles is decomposed into rotation and migration and calculated by MD simulation. By means of Peclet number, the effect of nanoparticle Brownian motion for thermal conductivity enhancement of nanofluids is discussed.
Humanoid Robot Simulator: A Realistic Dynamics Approach
Lima, José; Gonçalves, José; Costa, Paulo; Moreira, António
2008-01-01
This paper describes a humanoid robot simulator with realistic dynamics. As simulation is a powerful tool for speeding up the control software development, the suggested accurate simulator allows to accomplish this goal. The simulator, based on the Open Dynamics Engine and GLScene graphics library, provides instant visual feedback and allows the user to test any control strategy without damaging the real robot in the early stages of the development. The proposed simulator also captures some c...
Brownian Motion, "Diverse and Undulating"
Duplantier, Bertrand
2016-01-01
We describe in detail the history of Brownian motion, as well as the contributions of Einstein, Sutherland, Smoluchowski, Bachelier, Perrin and Langevin to its theory. The always topical importance in physics of the theory of Brownian motion is illustrated by recent biophysical experiments, where it serves, for instance, for the measurement of the pulling force on a single DNA molecule. In a second part, we stress the mathematical importance of the theory of Brownian motion, illustrated by two chosen examples. The by-now classic representation of the Newtonian potential by Brownian motion is explained in an elementary way. We conclude with the description of recent progress seen in the geometry of the planar Brownian curve. At its heart lie the concepts of conformal invariance and multifractality, associated with the potential theory of the Brownian curve itself.
Trefan, Gyorgy
1993-01-01
The goal of this thesis is to contribute to the ambitious program of the foundation of developing statistical physics using chaos. We build a deterministic model of Brownian motion and provide a microscopic derivation of the Fokker-Planck equation. Since the Brownian motion of a particle is the result of the competing processes of diffusion and dissipation, we create a model where both diffusion and dissipation originate from the same deterministic mechanism--the deterministic interaction of that particle with its environment. We show that standard diffusion which is the basis of the Fokker-Planck equation rests on the Central Limit Theorem, and, consequently, on the possibility of deriving it from a deterministic process with a quickly decaying correlation function. The sensitive dependence on initial conditions, one of the defining properties of chaos insures this rapid decay. We carefully address the problem of deriving dissipation from the interaction of a particle with a fully deterministic nonlinear bath, that we term the booster. We show that the solution of this problem essentially rests on the linear response of a booster to an external perturbation. This raises a long-standing problem concerned with Kubo's Linear Response Theory and the strong criticism against it by van Kampen. Kubo's theory is based on a perturbation treatment of the Liouville equation, which, in turn, is expected to be totally equivalent to a first-order perturbation treatment of single trajectories. Since the boosters are chaotic, and chaos is essential to generate diffusion, the single trajectories are highly unstable and do not respond linearly to weak external perturbation. We adopt chaotic maps as boosters of a Brownian particle, and therefore address the problem of the response of a chaotic booster to an external perturbation. We notice that a fully chaotic map is characterized by an invariant measure which is a continuous function of the control parameters of the map
Combinatorial fractal Brownian motion model
Institute of Scientific and Technical Information of China (English)
朱炬波; 梁甸农
2000-01-01
To solve the problem of how to determine the non-scaled interval when processing radar clutter using fractal Brownian motion (FBM) model, a concept of combinatorial FBM model is presented. Since the earth (or sea) surface varies diversely with space, a radar clutter contains several fractal structures, which coexist on all scales. Taking the combination of two FBMs into account, via theoretical derivation we establish a combinatorial FBM model and present a method to estimate its fractal parameters. The correctness of the model and the method is proved by simulation experiments and computation of practial data. Furthermore, we obtain the relationship between fractal parameters when processing combinatorial model with a single FBM model. Meanwhile, by theoretical analysis it is concluded that when combinatorial model is observed on different scales, one of the fractal structures is more obvious.
Simulation of Fault Zone Dynamics
Mora, P.; Abe, S.; Place, D.
2002-12-01
Particle models such as the discrete element model for granular assemblies and the lattice solid model provide a means to study the dynamics of fault zones. The lattice solid model was developed with the aim of progressively building up the capacity to simulate all relevent physical processes in fault zones. The present implementation of the model is able to simulate the dynamics of a granular lattice consisting of bonded or unbonded circular (2D) or spherical (3D) particles. Thermal effects (frictional hear generation, thermal expansion, heat flow) and pore fluid effects (heat induced pore pressure gradients and the consequent Darcian flow and impact on effective friction) can be modelled. Past work involving both circular particles and non-circular grains constructed as groups of bonded particles have demonstrated that grain shape has a fundamental impact on zero-th order behaviour. When circular particles are used, rolling is the most efficient means to accomodate slip of a simulated fault gouge layer leading to unrealistically low friction, typically around 0.2. This is consistent with laboratory results by Mair and Marone which have demonstrated that gouge consisting entirely of spherical beads shows a lower coefficient of friction than gouge containing irregular shaped particles. Recent work comparing quasi-2D laboratory results using pasta (Marone) with 2D numerical results (Morgan) have confirmed that numerical and laboratory results with circular ``particles'' are in agreement. When irregular grains are modelled at the lowest scale, the friction of simulated gouge layers matches with laboratory observations of rock friction (μ ~ 0.6) and is insentitive to the value used for interparticle friction (Mora et al, 2000). This indicates a self-regulation mechanism is occurring in which the group behaviour of the gouge layer remains constant at around 0.6 by balancing the amount of slip and rolling of grains within the gouge layer. A limitation of these studies
Brownian semi-stationary processes, turbulence and smooth processes
DEFF Research Database (Denmark)
Urbina, José Ulises Márquez
This thesis analysis the use of Brownian semi-stationary (BSS) processes to model the main statistical features present in turbulent time series, and some asymptotic properties of certain classes of smooth processes. Turbulence is a complex phenomena governed by the Navier-Stokes equations. These...... equations do not represent a fully functional model and, consequently, it has been necessary to develop phenomenological models capturing main aspects of turbulent dynamics. The BSS processes were proposed as an option to model turbulent time series. In this thesis we proved, through a simulation....... We also studied the distributional properties of the increments of BSS processes with the intent to better understand why the BSS processes seem to accurately reproduce the temporal turbulent dynamics. BSS processes in general are not semimartingales. However, there are conditions which make a BSS...
QUANTUM STOCHASTIC PROCESSES: BOSON AND FERMION BROWNIAN MOTION
Directory of Open Access Journals (Sweden)
A.E.Kobryn
2003-01-01
Full Text Available Dynamics of quantum systems which are stochastically perturbed by linear coupling to the reservoir can be studied in terms of quantum stochastic differential equations (for example, quantum stochastic Liouville equation and quantum Langevin equation. In order to work it out one needs to define the quantum Brownian motion. As far as only its boson version has been known until recently, in the present paper we present the definition which makes it possible to consider the fermion Brownian motion as well.
Holographic Brownian Motion at Finite Density
Banerjee, Pinaki
2015-01-01
We study holographic Brownian motion of a heavy charged particle at zero and small (but finite) temperature in presence of finite density. We are primarily interested in the dynamics at (near) zero temperature which is holographically described by motion of a fundamental string in an (near-) extremal RN black hole. We compute analytically the functional form of retarded Green's function and also compare that numerically at leading order in small frequency.
Brownian particles in supramolecular polymer solutions
Gucht, van der, J.; Besseling, N.A.M.; Knoben, W.; Bouteiller, L; Cohen Stuart, M. A.
2003-01-01
The Brownian motion of colloidal particles embedded in solutions of hydrogen-bonded supramolecular polymers has been studied using dynamic light scattering. At short times, the motion of the probe particles is diffusive with a diffusion coefficient equal to that in pure solvent. At intermediate time scales the particles are slowed down as a result of trapping in elastic cages formed by the polymer chains, while at longer times the motion is diffusive again, but with a much smaller diffusion c...
Enabling Strain Hardening Simulations with Dislocation Dynamics
Energy Technology Data Exchange (ETDEWEB)
Arsenlis, A; Cai, W
2006-12-20
Numerical algorithms for discrete dislocation dynamics simulations are investigated for the purpose of enabling strain hardening simulations of single crystals on massively parallel computers. The algorithms investigated include the /(N) calculation of forces, the equations of motion, time integration, adaptive mesh refinement, the treatment of dislocation core reactions, and the dynamic distribution of work on parallel computers. A simulation integrating all of these algorithmic elements using the Parallel Dislocation Simulator (ParaDiS) code is performed to understand their behavior in concert, and evaluate the overall numerical performance of dislocation dynamics simulations and their ability to accumulate percents of plastic strain.
Frustrated Brownian Motion of Nonlocal Solitary Waves
International Nuclear Information System (INIS)
We investigate the evolution of solitary waves in a nonlocal medium in the presence of disorder. By using a perturbational approach, we show that an increasing degree of nonlocality may largely hamper the Brownian motion of self-trapped wave packets. The result is valid for any kind of nonlocality and in the presence of nonparaxial effects. Analytical predictions are compared with numerical simulations based on stochastic partial differential equations.
The open quantum Brownian motions
International Nuclear Information System (INIS)
Using quantum parallelism on random walks as the original seed, we introduce new quantum stochastic processes, the open quantum Brownian motions. They describe the behaviors of quantum walkers—with internal degrees of freedom which serve as random gyroscopes—interacting with a series of probes which serve as quantum coins. These processes may also be viewed as the scaling limit of open quantum random walks and we develop this approach along three different lines: the quantum trajectory, the quantum dynamical map and the quantum stochastic differential equation. We also present a study of the simplest case, with a two level system as an internal gyroscope, illustrating the interplay between the ballistic and diffusive behaviors at work in these processes. Notation Hz: orbital (walker) Hilbert space, CZ in the discrete, L2(R) in the continuum Hc: internal spin (or gyroscope) Hilbert space Hsys=Hz⊗Hc: system Hilbert space Hp: probe (or quantum coin) Hilbert space, Hp=C2 ρttot: density matrix for the total system (walker + internal spin + quantum coins) ρ-bar t: reduced density matrix on Hsys: ρ-bar t=∫dxdy ρ-bar t(x,y)⊗|x〉z〈y| ρ-hat t: system density matrix in a quantum trajectory: ρ-hat t=∫dxdy ρ-hat t(x,y)⊗|x〉z〈y|. If diagonal and localized in position: ρ-hat t=ρt⊗|Xt〉z〈Xt| ρt: internal density matrix in a simple quantum trajectory Xt: walker position in a simple quantum trajectory Bt: normalized Brownian motion ξt, ξt†: quantum noises (paper)
Molecular dynamics simulation by atomic mass weighting
Mao, Boryeu; Friedman, Alan R.
1990-01-01
A molecular dynamics-based simulation method in which atomic masses are weighted is described. Results from this method showed that the capability for conformation search in molecular dynamics simulation of a short peptide (FMRF-amide) is significantly increased by mass weighting.
Directory of Open Access Journals (Sweden)
Satoshi Ota
2016-09-01
Full Text Available The dependence of magnetic relaxation on particle parameters, such as the size and anisotropy, has been conventionally discussed. In addition, the influences of external conditions, such as the intensity and frequency of the applied field, the surrounding viscosity, and the temperature on the magnetic relaxation have been researched. According to one of the basic theories regarding magnetic relaxation, the faster type of relaxation dominates the process. However, in this study, we reveal that Brownian and Néel relaxations coexist and that Brownian relaxation can occur after Néel relaxation despite having a longer relaxation time. To understand the mechanisms of Brownian rotation, alternating current (AC hysteresis loops were measured in magnetic fluids of different viscosities. These loops conveyed the amplitude and phase delay of the magnetization. In addition, the intrinsic loss power (ILP was calculated using the area of the AC hysteresis loops. The ILP also showed the magnetization response regarding the magnetic relaxation over a wide frequency range. To develop biomedical applications of magnetic nanoparticles, such as hyperthermia and magnetic particle imaging, it is necessary to understand the mechanisms of magnetic relaxation.
Accelerated molecular dynamics simulations of protein folding
Miao, Y.; Feixas, F; Eun, C; McCammon, JA
2015-01-01
© 2015 Wiley Periodicals, Inc. Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native ...
Speckle Patterns and 2-Dimensional Brownian Motion
International Nuclear Information System (INIS)
We present the results of a Monte Carlo simulation of Brownian Motion on a 2-dimensional lattice with nearest-neighbor interactions described by a linear model. These nearest-neighbor interactions lead to a spatial variance structure on the lattice. The resulting Brownian pattern fluctuates in value from point to point in a manner characteristic of a stationary stochastic process. The value at a lattice point is interpreted as an intensity level. The difference in values in neighboring cells produces a fluctuating intensity pattern on the lattice. Changing the size of the mesh changes the relative size of the speckles. Increasing the mesh size tends to average out the intensity in the direction of the mean of the stationary process. (Author)
Modeling collective emotions: a stochastic approach based on Brownian agents
International Nuclear Information System (INIS)
We develop a agent-based framework to model the emergence of collective emotions, which is applied to online communities. Agents individual emotions are described by their valence and arousal. Using the concept of Brownian agents, these variables change according to a stochastic dynamics, which also considers the feedback from online communication. Agents generate emotional information, which is stored and distributed in a field modeling the online medium. This field affects the emotional states of agents in a non-linear manner. We derive conditions for the emergence of collective emotions, observable in a bimodal valence distribution. Dependent on a saturated or a super linear feedback between the information field and the agent's arousal, we further identify scenarios where collective emotions only appear once or in a repeated manner. The analytical results are illustrated by agent-based computer simulations. Our framework provides testable hypotheses about the emergence of collective emotions, which can be verified by data from online communities. (author)
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Jahn, S.; P. A. Madden
2008-01-01
The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q) from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω) from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the ...
Dynamics in inhomogeneous liquids and glasses via the test particle limit
Archer, Andrew J.; Hopkins, Paul; Schmidt, Matthias
2006-01-01
We show that one may view the self and the distinct part of the van Hove dynamic correlation function of a simple fluid as the one-body density distributions of a binary mixture that evolve in time according to dynamical density functional theory. For a test case of soft core Brownian particles the theory yields results for the van Hove function that agree quantitatively with those of our Brownian dynamics computer simulations. At sufficiently high densities the free energy landscape underlyi...
Particle dynamics in two-dimensional random-energy landscapes: Experiments and simulations
Evers, Florian; Zunke, Christoph; Hanes, Richard D. L.; Bewerunge, Jörg; Ladadwa, Imad; Heuer, Andreas; Egelhaaf, Stefan U.
2013-08-01
The dynamics of individual colloidal particles in random potential energy landscapes was investigated experimentally and by Monte Carlo simulations. The value of the potential at each point in the two-dimensional energy landscape follows a Gaussian distribution. The width of the distribution, and hence the degree of roughness of the energy landscape, was varied and its effect on the particle dynamics studied. This situation represents an example of Brownian dynamics in the presence of disorder. In the experiments, the energy landscapes were generated optically using a holographic setup with a spatial light modulator, and the particle trajectories were followed by video microscopy. The dynamics is characterized using, e.g., the time-dependent diffusion coefficient, the mean squared displacement, the van Hove function, and the non-Gaussian parameter. In both experiments and simulations the dynamics is initially diffusive, showing an extended subdiffusive regime at intermediate times before diffusive motion is recovered at very long times. The dependence of the long-time diffusion coefficient on the width of the Gaussian distribution agrees with theoretical predictions. Compared to the dynamics in a one-dimensional potential energy landscape, the localization at intermediate times is weaker and the diffusive regime at long times reached earlier, which is due to the possibility to avoid local maxima in two-dimensional energy landscapes.
Intrinsic and extrinsic measurement for Brownian motion
International Nuclear Information System (INIS)
Based upon the Smoluchowski equation on curved manifolds, three physical observables are considered for Brownian displacement, namely geodesic displacement s, Euclidean displacement δR, and projected displacement δR⊥. The Weingarten–Gauss equations are used to calculate the mean-square Euclidean displacements in the short-time regime. Our findings show that from an extrinsic point of view the geometry of the space affects the Brownian motion in such a way that the particle’s diffusion is decelerated, contrasting with the intrinsic point of view where dynamics is controlled by the sign of the Gaussian curvature (Castro-Villarreal, 2010 J. Stat. Mech. P08006). Furthermore, it is possible to give exact formulas for 〈δR〉 and 〈δR2〉 on spheres and minimal surfaces, which are valid for all values of time. In the latter case, surprisingly, Brownian motion corresponds to the usual diffusion in flat geometries, albeit minimal surfaces have non-zero Gaussian curvature. Finally, the two-dimensional case is emphasized due to its close relation to surface self-diffusion in fluid membranes. (paper)
Brownian Motion Theory and Experiment
Basu, K; Basu, Kasturi; Baishya, Kopinjol
2003-01-01
Brownian motion is the perpetual irregular motion exhibited by small particles immersed in a fluid. Such random motion of the particles is produced by statistical fluctuations in the collisions they suffer with the molecules of the surrounding fluid. Brownian motion of particles in a fluid (like milk particles in water) can be observed under a microscope. Here we describe a simple experimental set-up to observe Brownian motion and a method of determining the diffusion coefficient of the Brownian particles, based on a theory due to Smoluchowski. While looking through the microscope we focus attention on a fixed small volume, and record the number of particles that are trapped in that volume, at regular intervals of time. This gives us a time-series data, which is enough to determine the diffusion coefficient of the particles to a good degree of accuracy.
Energy Technology Data Exchange (ETDEWEB)
Agusdinata, Datu Buyung, E-mail: bagusdinata@niu.edu; Amouie, Mahbod [Northern Illinois University, Department of Industrial & Systems Engineering and Environment, Sustainability, & Energy Institute (United States); Xu, Tao [Northern Illinois University, Department of Chemistry and Biochemistry (United States)
2015-01-15
Due to their favorable electrical and optical properties, quantum dots (QDs) nanostructures have found numerous applications including nanomedicine and photovoltaic cells. However, increased future production, use, and disposal of engineered QD products also raise concerns about their potential environmental impacts. The objective of this work is to establish a modeling framework for predicting the diffusion dynamics and concentration of toxic materials released from Trioctylphosphine oxide-capped CdSe. To this end, an agent-based model simulation with reaction kinetics and Brownian motion dynamics was developed. Reaction kinetics is used to model the stability of surface capping agent particularly due to oxidation process. The diffusion of toxic Cd{sup 2+} ions in aquatic environment was simulated using an adapted Brownian motion algorithm. A calibrated parameter to reflect sensitivity to reaction rate is proposed. The model output demonstrates the stochastic spatial distribution of toxic Cd{sup 2+} ions under different values of proxy environmental factor parameters. With the only chemistry considered was oxidation, the simulation was able to replicate Cd{sup 2+} ion release from Thiol-capped QDs in aerated water. The agent-based method is the first to be developed in the QDs application domain. It adds both simplicity of the solubility and rate of release of Cd{sup 2+} ions and complexity of tracking of individual atoms of Cd at the same time.
International Nuclear Information System (INIS)
Due to their favorable electrical and optical properties, quantum dots (QDs) nanostructures have found numerous applications including nanomedicine and photovoltaic cells. However, increased future production, use, and disposal of engineered QD products also raise concerns about their potential environmental impacts. The objective of this work is to establish a modeling framework for predicting the diffusion dynamics and concentration of toxic materials released from Trioctylphosphine oxide-capped CdSe. To this end, an agent-based model simulation with reaction kinetics and Brownian motion dynamics was developed. Reaction kinetics is used to model the stability of surface capping agent particularly due to oxidation process. The diffusion of toxic Cd2+ ions in aquatic environment was simulated using an adapted Brownian motion algorithm. A calibrated parameter to reflect sensitivity to reaction rate is proposed. The model output demonstrates the stochastic spatial distribution of toxic Cd2+ ions under different values of proxy environmental factor parameters. With the only chemistry considered was oxidation, the simulation was able to replicate Cd2+ ion release from Thiol-capped QDs in aerated water. The agent-based method is the first to be developed in the QDs application domain. It adds both simplicity of the solubility and rate of release of Cd2+ ions and complexity of tracking of individual atoms of Cd at the same time
On collisions of Brownian particles
Ichiba, Tomoyuki; Karatzas, Ioannis
2010-01-01
We examine the behavior of $n$ Brownian particles diffusing on the real line with bounded, measurable drift and bounded, piecewise continuous diffusion coefficients that depend on the current configuration of particles. Sufficient conditions are established for the absence and for the presence of triple collisions among the particles. As an application to the Atlas model for equity markets, we study a special construction of such systems of diffusing particles using Brownian motions with refl...
Archimedes’ principle for Brownian liquid
Burdzy, Krzysztof; Chen, Zhen-Qing; Pal, Soumik
2011-01-01
We consider a family of hard core objects moving as independent Brownian motions confined to a vessel by reflection. These are subject to gravitational forces modeled by drifts. The stationary distribution for the process has many interesting implications, including an illustration of the Archimedes' principle. The analysis rests on constructing reflecting Brownian motion with drift in a general open connected domain and studying its stationary distribution. In dimension two we utilize known ...
Archimedes' principle for Brownian liquid
Burdzy, Krzysztof; Pal, Soumik
2009-01-01
We consider a family of hard core objects moving as independent Brownian motions confined to a vessel by reflection. These are subject to gravitational forces modeled by drifts. The stationary distribution for the process has many interesting implications, including an illustration of the Archimedes' principle. The analysis rests on constructing reflecting Brownian motion with drift in a general open connected domain and studying its stationary distribution. In dimension two we utilize known results about sphere packing.
A qualitative dynamical model for cardiotocography simulation
Illanes, Alfredo; Haritopoulos, Michel; Robles, Felipe; Guerra, Francisco
2015-01-01
The purpose of this work is to present a new mathematical model for fetal monitoring simulation. It involves the simultaneous generation of fetal heart rate and maternal uterine contraction signals through a parametrical model. This model allows the generation of the main fetal monitoring dynamics including fetal movements, acceleration and deceleration of the heart rate and the dynami-cal adjustment of fetal heart rate following an uterine contraction. Simulated tracings were analyzed by spe...
Molecular Dynamic Simulation on High Performance Infrastrucutres
Bergant, Anže
2016-01-01
This thesis covers comparison between different computer platforms of high performance computing while performing molecular dynamics simulations, which falls under very complex problems and needs lots of processing power. Our goal was to critically evaluate different platforms while solving molecular dynamics, so we used 1 to 16 processor cores on a computer cluster and one and two graphics processing units (GPU) for simulations. The results will be used while planning on buying new computer ...
Visualizing Structure and Dynamics of Disaccharide Simulations
Energy Technology Data Exchange (ETDEWEB)
Matthews, J. F.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.
2012-01-01
We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.
Molecular dynamics simulation of impact test
Energy Technology Data Exchange (ETDEWEB)
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Melting behaviour of gold-platinum nanoalloy clusters by molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Ong, Yee Pin; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)
2015-04-24
The melting behavior of bimetallic gold-platinum nanoclusters is studied by applying Brownian-type isothermal molecular dynamics (MD) simulation, a program modified from the cubic coupling scheme (CCS). The process begins with the ground-state structures obtained from global minimum search algorithm and proceeds with the investigation of the effect of temperature on the thermal properties of gold-platinum nanoalloy clusters. N-body Gupta potential has been employed in order to account for the interactions between gold and platinum atoms. The ground states of the nanoalloy clusters, which are core-shell segregated, are heated until they become thermally segregated. The detailed melting mechanism of the nanoalloy clusters is studied via this approach to provide insight into the thermal stability of the nanoalloy clusters.
Melting behaviour of gold-platinum nanoalloy clusters by molecular dynamics simulations
International Nuclear Information System (INIS)
The melting behavior of bimetallic gold-platinum nanoclusters is studied by applying Brownian-type isothermal molecular dynamics (MD) simulation, a program modified from the cubic coupling scheme (CCS). The process begins with the ground-state structures obtained from global minimum search algorithm and proceeds with the investigation of the effect of temperature on the thermal properties of gold-platinum nanoalloy clusters. N-body Gupta potential has been employed in order to account for the interactions between gold and platinum atoms. The ground states of the nanoalloy clusters, which are core-shell segregated, are heated until they become thermally segregated. The detailed melting mechanism of the nanoalloy clusters is studied via this approach to provide insight into the thermal stability of the nanoalloy clusters
Noise-to-signal transition of a Brownian particle in the cubic potential: I. general theory
Filip, Radim; Zemánek, Pavel
2016-06-01
The noise-to-signal transitions are very interesting processes in physics, as they might transform environmental noise to useful mechanical effects. We theoretically analyze stochastic noise-to-signal transition of overdamped Brownian motion of a particle in the cubic potential. The particle reaches thermal equilibrium with its environment in the quadratic potential which is suddenly swapped to the cubic potential. We predict a simultaneous increase of both the displacement and signal-to-noise ratio in the cubic potential for the position linearly powered by the temperature of the particle environment. The short-time analysis and numerical simulations fully confirm different dynamical regimes of this noise-to-signal transition.
Anomalous Brownian refrigerator
Rana, Shubhashis; Pal, P. S.; Saha, Arnab; Jayannavar, A. M.
2016-02-01
We present a detailed study of a Brownian particle driven by Carnot-type refrigerating protocol operating between two thermal baths. Both the underdamped as well as the overdamped limits are investigated. The particle is in a harmonic potential with time-periodic strength that drives the system cyclically between the baths. Each cycle consists of two isothermal steps at different temperatures and two adiabatic steps connecting them. Besides working as a stochastic refrigerator, it is shown analytically that in the quasistatic regime the system can also act as stochastic heater, depending on the bath temperatures. Interestingly, in non-quasistatic regime, our system can even work as a stochastic heat engine for certain range of cycle time and bath temperatures. We show that the operation of this engine is not reliable. The fluctuations of stochastic efficiency/coefficient of performance (COP) dominate their mean values. Their distributions show power law tails, however the exponents are not universal. Our study reveals that microscopic machines are not the microscopic equivalent of the macroscopic machines that we come across in our daily life. We find that there is no one to one correspondence between the performance of our system under engine protocol and its reverse.
Martínez, I. A.; Roldán, É.; Dinis, L.; Petrov, D.; Parrondo, J. M. R.; Rica, R. A.
2016-01-01
The Carnot cycle imposes a fundamental upper limit to the efficiency of a macroscopic motor operating between two thermal baths. However, this bound needs to be reinterpreted at microscopic scales, where molecular bio-motors and some artificial micro-engines operate. As described by stochastic thermodynamics, energy transfers in microscopic systems are random and thermal fluctuations induce transient decreases of entropy, allowing for possible violations of the Carnot limit. Here we report an experimental realization of a Carnot engine with a single optically trapped Brownian particle as the working substance. We present an exhaustive study of the energetics of the engine and analyse the fluctuations of the finite-time efficiency, showing that the Carnot bound can be surpassed for a small number of non-equilibrium cycles. As its macroscopic counterpart, the energetics of our Carnot device exhibits basic properties that one would expect to observe in any microscopic energy transducer operating with baths at different temperatures. Our results characterize the sources of irreversibility in the engine and the statistical properties of the efficiency--an insight that could inspire new strategies in the design of efficient nano-motors.
Molecular dynamics simulations using graphics processing units
Baker, J.A.; Hirst, J.D.
2011-01-01
It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation com...
Generalization of Brownian Motion with Autoregressive Increments
Fendick, Kerry
2011-01-01
This paper introduces a generalization of Brownian motion with continuous sample paths and stationary, autoregressive increments. This process, which we call a Brownian ray with drift, is characterized by three parameters quantifying distinct effects of drift, volatility, and autoregressiveness. A Brownian ray with drift, conditioned on its state at the beginning of an interval, is another Brownian ray with drift over the interval, and its expected path over the interval is a ray with a slope that depends on the conditioned state. This paper shows how Brownian rays can be applied in finance for the analysis of queues or inventories and the valuation of options. We model a queue's net input process as a superposition of Brownian rays with drift and derive the transient distribution of the queue length conditional on past queue lengths and on past states of the individual Brownian rays comprising the superposition. The transient distributions of Regulated Brownian Motion and of the Regulated Brownian Bridge are...
Nanofluidic Brownian Ratchet via atomically-stepped surfaces
Rahmani, Amir; Colosqui, Carlos
2015-11-01
Theoretical analysis and fully atomistic molecular dynamics simulations reveal a Brownian ratchet mechanism by which thermal motion can drive the directional displacement of liquids confined in micro- or nanoscale channels and pores. The particular systems discussed in this talk consist of two immiscible liquids confined in a slit-like nanochannel with atomically-stepped surfaces. Mean displacement rates reported in molecular dynamics simulations are in close agreement with theoretical predictions via analytical solution of a Smoluchowski equation for the probability density of the position of the liquid-liquid interface. The direction of the thermally-driven displacement of liquid is determined by the nanostructure surface geometry and thus imbibition or drainage can occur against the direction of action of capillary forces. The studied surface nanostructure with directional asymmetry can control the dynamics of wetting processes such as capillary filling, wicking, and imbibition in porous materials. The proposed physical mechanisms and derived analytical expressions can be applied to design nanofluidic and microfluidic devices for passive handling and separation.
Discrete dislocation dynamics simulations in a cylinder
Li, Maosheng; Gao, Chan; Xu, Jianing
2015-02-01
Mechanical properties of material are closely related to the motion of dislocations, and predicting the interactions and resulting collective motion of dislocations is a major task in understanding and modelling plastically deforming materials. A discrete dislocation dynamics model is used to describe the orientation substructure within the microstructure. Discrete dislocation dynamics simulations in three dimensions have been used to examine the role of dislocation multiplication and mobility on the plasticity in small samples under uniaxial compression. In this paper we describe the application of the dislocation dynamics simulations in a cylindrical geometry. The boundary conditions for the simulation were estimated from the distribution of the geometrically necessary dislocation density which was obtained from the orientation map. Numerical studies benchmark could validate the accuracy of the algorithms and the importance of handling the singularity correctly. The results of the simulation explain the formation of the experimentally observed substructure.
Spin dynamics simulations at AGS
Energy Technology Data Exchange (ETDEWEB)
Huang, H.; MacKay, W.W.; Meot, F.; Roser, T.
2010-05-23
To preserve proton polarization through acceleration, it is important to have a correct model of the process. It has been known that with the insertion of the two helical partial Siberian snakes in the Alternating Gradient Synchrotron (AGS), the MAD model of AGS can not deal with a field map with offset orbit. The stepwise ray-tracing code Zgoubi provides a tool to represent the real electromagnetic fields in the modeling of the optics and spin dynamics for the AGS. Numerical experiments of resonance crossing, including spin dynamics in presence of the snakes and Q-jump, have been performed in AGS lattice models, using Zgoubi. This contribution reports on various results so obtained.
Harmonic functions on Walsh's Brownian motion
Jehring, Kristin Elizabeth
2009-01-01
In this dissertation we examine a variation of two- dimensional Brownian motion introduced in 1978 by Walsh. Walsh's Brownian motion can be described as a Brownian motion on the spokes of a (rimless) bicycle wheel. We will construct such a process by randomly assigning an angle to the excursions of a reflecting Brownian motion from 0. With this construction we see that Walsh's Brownian motion in R² behaves like one-dimensional Brownian motion away from the origin, but at the origin behaves di...
Dynamics of individual colloidal particles in one-dimensional random potentials: a simulation study.
Hanes, Richard D L; Egelhaaf, Stefan U
2012-11-21
Using Monte Carlo simulations, individual Brownian particles have been investigated in a one-dimensional random energy landscape whose energy levels are selected from a Gaussian distribution. The standard deviation of the distribution determines the roughness of the noise-like potential and was varied in the simulations. After initialization, which was done by an instantaneous or infinitely slow (annealed) quench, the particle dynamics were followed. They were characterized by a number of parameters, such as the mean squared displacement, the time dependent diffusion coefficient, the non-Gaussian parameter, and the van Hove function. The dynamics exhibit different regimes: at very short times superdiffusion, followed by normal diffusion, and subsequently an extended period of subdiffusive dynamics due to localization within the minima of the potential, and finally, after a very slow approach towards the long-time limit, again diffusion with a significantly reduced diffusion coefficient. The long-time diffusion coefficient is consistent with theoretical predictions while no predictions exist for the intermediate times. Nevertheless, over the whole time range, the simulation results are in agreement with recent experimental findings on colloidal particles in a random potential created by a holographic optical setup. PMID:23114221
Híjar, Humberto
2015-02-01
We study the Brownian motion of a particle bound by a harmonic potential and immersed in a fluid with a uniform shear flow. We describe this problem first in terms of a linear Fokker-Planck equation which is solved to obtain the probability distribution function for finding the particle in a volume element of its associated phase space. We find the explicit form of this distribution in the stationary limit and use this result to show that both the equipartition law and the equation of state of the trapped particle are modified from their equilibrium form by terms increasing as the square of the imposed shear rate. Subsequently, we propose an alternative description of this problem in terms of a generalized Langevin equation that takes into account the effects of hydrodynamic correlations and sound propagation on the dynamics of the trapped particle. We show that these effects produce significant changes, manifested as long-time tails and resonant peaks, in the equilibrium and nonequilibrium correlation functions for the velocity of the Brownian particle. We implement numerical simulations based on molecular dynamics and multiparticle collision dynamics, and observe a very good quantitative agreement between the predictions of the model and the numerical results, thus suggesting that this kind of numerical simulations could be used as complement of current experimental techniques. PMID:25768490
Ilg, Patrick; Karlin, Iliya V.
2004-01-01
A method for the combination of microscopic and macroscopic simulations is developed which is based on the invariance of the macroscopic relative to the microscopic dynamics. The method recognizes the onset and breakdown of the macroscopic description during the integration. We apply this method to the case of ferrofluid dynamics, where it switches between direct Brownian dynamics simulations and integration of the constitutive equation.
Sensitivity Analysis of Fire Dynamics Simulation
DEFF Research Database (Denmark)
Brohus, Henrik; Nielsen, Peter V.; Petersen, Arnkell J.; Sommerlund-Larsen, Kim
2007-01-01
In case of fire dynamics simulation requirements to reliable results are most often very high due to the severe consequences of erroneous results. At the same time it is a well known fact that fire dynamics simulation constitutes rather complex physical phenomena which apart from flow and energy...... equations require solution of the issues of combustion and gas radiation to mention a few. This paper performs a sensitivity analysis of a fire dynamics simulation on a benchmark case where measurement results are available for comparison. The analysis is performed using the method of Elementary Effects...... (Morris method). The parameters considered are selected among physical parameters and program specific parameters. The influence on the calculation result as well as the CPU time is considered. It is found that the result is highly sensitive to many parameters even though the sensitivity varies...
On the Generalized Brownian Motion and its Applications in Finance
DEFF Research Database (Denmark)
Høg, Esben; Frederiksen, Per; Schiemert, Daniel
This paper deals with dynamic term structure models (DTSMs) and proposes a new way to handle the limitation of the classical affine models. In particular, the paper expands the exibility of the DTSMs by applying generalized Brownian motions with dependent increments as the governing force of the ...
Dynamical structure of fluid mercury: Molecular-dynamics simulations
Hoshino, Kozo; Tanaka, Shunichiro; Shimojo, Fuyuki
2007-01-01
We have carried out molecular-dynamics simulations for nonmetallic fluid mercury in liquid and vapor phases using a Lennard-Jones type effective potential and shown that the structure factors S(Q) and the dynamic structure factors S(Q, omega) of nonmetallic fluid mercury obtained by our MD simulations are in good agreement with recent X-ray diffraction and inelastic X-ray scattering experiments. We conclude from these results that, though the fluid mercury which shows a metal-nonmetal transit...
Entropic forces in Brownian motion
Roos, Nico
2013-01-01
The interest in the concept of entropic forces has risen considerably since E. Verlinde proposed to interpret the force in Newton s second law and Gravity as entropic forces. Brownian motion, the motion of a small particle (pollen) driven by random impulses from the surrounding molecules, may be the first example of a stochastic process in which such forces are expected to emerge. In this note it is shown that at least two types of entropic motion can be identified in the case of 3D Brownian motion (or random walk). This yields simple derivations of known results of Brownian motion, Hook s law and, applying an external (nonradial) force, Curie s law and the Langevin-Debye equation.
Entropic forces in Brownian motion
Roos, Nico
2014-12-01
Interest in the concept of entropic forces has risen considerably since Verlinde proposed in 2011 to interpret the force in Newton's second law and gravity as entropic forces. Brownian motion—the motion of a small particle (pollen) driven by random impulses from the surrounding molecules—may be the first example of a stochastic process in which such forces are expected to emerge. In this article, it is shown that at least two types of entropic force can be identified in three-dimensional Brownian motion. This analysis yields simple derivations of known results of Brownian motion, Hooke's law, and—applying an external (non-radial) force—Curie's law and the Langevin-Debye equation.
Methane in carbon nanotube - molecular dynamics simulation
Bartuś, Katarzyna; Bródka, Aleksander
2011-01-01
Abstract The behaviour of methane molecules inside carbon nanotube at room temperature is studied using classical molecular dynamics simulations. A methane molecule is represented either by a shapeless super-atom or by rigid set of 5 interaction centres localised on atoms. Different loadings of methane molecules ranging from the dense gas density to the liquid density, and the influence of flexibility of the CNT on structural and dynamics properties of confined molecules are consid...
Dynamic Fracture Simulations of Explosively Loaded Cylinders
Energy Technology Data Exchange (ETDEWEB)
Arthur, Carly W. [Univ. of California, Davis, CA (United States). Dept. of Civil and Environmental Engineering; Goto, D. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-11-30
This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.
Cyclotron beam dynamic simulations in MATLAB
International Nuclear Information System (INIS)
MATLAB is useful for beam dynamic simulations in cyclotrons. Programming in an easy-to-use environment permits creation of models in a short space of time. Advanced graphical tools of MATLAB give good visualization features to created models. The beam dynamic modeling results with an example of two different cyclotron designs are presented. Programming with MATLAB opens wide possibilities of the development of the complex program, able to perform complete block of calculations for the design of the accelerators
Quantum Brownian motion model for the stock market
Meng, Xiangyi; Zhang, Jian-Wei; Guo, Hong
2016-06-01
It is believed by the majority today that the efficient market hypothesis is imperfect because of market irrationality. Using the physical concepts and mathematical structures of quantum mechanics, we construct an econophysical framework for the stock market, based on which we analogously map massive numbers of single stocks into a reservoir consisting of many quantum harmonic oscillators and their stock index into a typical quantum open system-a quantum Brownian particle. In particular, the irrationality of stock transactions is quantitatively considered as the Planck constant within Heisenberg's uncertainty relationship of quantum mechanics in an analogous manner. We analyze real stock data of Shanghai Stock Exchange of China and investigate fat-tail phenomena and non-Markovian behaviors of the stock index with the assistance of the quantum Brownian motion model, thereby interpreting and studying the limitations of the classical Brownian motion model for the efficient market hypothesis from a new perspective of quantum open system dynamics.
Simulating coronal condensation dynamics in 3D
Moschou, S P; Xia, C; Fang, X
2015-01-01
We present numerical simulations in 3D settings where coronal rain phenomena take place in a magnetic configuration of a quadrupolar arcade system. Our simulation is a magnetohydrodynamic simulation including anisotropic thermal conduction, optically thin radiative losses, and parametrised heating as main thermodynamical features to construct a realistic arcade configuration from chromospheric to coronal heights. The plasma evaporation from chromospheric and transition region heights eventually causes localised runaway condensation events and we witness the formation of plasma blobs due to thermal instability, that evolve dynamically in the heated arcade part and move gradually downwards due to interchange type dynamics. Unlike earlier 2.5D simulations, in this case there is no large scale prominence formation observed, but a continuous coronal rain develops which shows clear indications of Rayleigh-Taylor or interchange instability, that causes the denser plasma located above the transition region to fall do...
Dynamic Simulations of Advanced Fuel Cycles
Energy Technology Data Exchange (ETDEWEB)
Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire
2011-03-01
Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the U.S. Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.
Massively-Parallel Dislocation Dynamics Simulations
Energy Technology Data Exchange (ETDEWEB)
Cai, W; Bulatov, V V; Pierce, T G; Hiratani, M; Rhee, M; Bartelt, M; Tang, M
2003-06-18
Prediction of the plastic strength of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of the existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, in order to be statistically representative and to reproduce experimentally observed microstructures. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss the general aspects of this code that make such large scale simulations possible, as well as a few initial simulation results.
Winding statistics of a Brownian particle on a ring
International Nuclear Information System (INIS)
We consider a Brownian particle moving on a ring. We study the probability distributions of the total number of turns and the net number of counter-clockwise turns the particle makes until time t. Using a method based on the renewal properties of a Brownian walker, we find exact analytical expressions of these distributions. This method serves as an alternative to the standard path integral techniques which are not always easily adaptable for certain observables. For large t, we show that these distributions have Gaussian scaling forms. We also compute large deviation functions associated to these distributions characterizing atypically large fluctuations. We provide numerical simulations in support of our analytical results. (paper)
Dynamic simulation of a high efficiency building
Dot Bardolet, Núria
2009-01-01
The dynamic simulation of the heat transfer between buildings and their environment is situdied through the software TRNSYS. First, a very simple building is considered and the energy demand for heating evaluated through TRNSYS is compared with that obtained by apllying the Italian Standard UNI TS 11300-1:2008. This excersise has the purpose of verifying the correct use of the simulation program. Then, the annual energy demand for heating, cooling and humidity control, with reference to a wel...
Feynman Rules For Brownian Motion
Hatamian, S T
2003-01-01
We present a perturbation theory extending a prescription due to Feynman for computing the probability density function in Brownian-motion. The method used, can be applied to a wide variety of otherwise difficult circumstances in Brownian-motion. The exact moments and kurtosis, if not the distribution itself, for many important cases can be summed for arbitrary times. As expected, the behavior at early time regime, for the sample processes considered, deviate significantly from the usual diffusion theory; a fact with important consequences in various applications such as financial physics. A new class of functions dubbed "Damped-exponential-integrals" are also identified.
Brownian movement and molecular reality
Perrin, Jean
2005-01-01
How do we know that molecules really exist? An important clue came from Brownian movement, a concept developed in 1827 by botanist Robert Brown, who noticed that tiny objects like pollen grains shook and moved erratically when viewed under a microscope. Nearly 80 years later, in 1905, Albert Einstein explained this ""Brownian motion"" as the result of bombardment by molecules. Einstein offered a quantitative explanation by mathematically estimating the average distance covered by the particles over time as a result of molecular bombardment. Four years later, Jean Baptiste Perrin wrote Brownia
Brownian molecular rotors: Theoretical design principles and predicted realizations
Schönborn, Jan Boyke; Herges, Rainer; Hartke, Bernd
2009-01-01
We propose simple design concepts for molecular rotors driven by Brownian motion and external photochemical switching. Unidirectionality and efﬁciency of the motion is measured by explicit simulations. Two different molecular scaffolds are shown to yield viable molecular rotors when decorated with suitable substituents.
Brownian colloidal particles: Ito, Stratonovich, or a different stochastic interpretation
Sancho, J. M.
2011-12-01
Recent experiments on Brownian colloidal particles have been studied theoretically in terms of overdamped Langevin equations with multiplicative white noise using an unconventional stochastic interpretation. Complementary numerical simulations of the same system are well described using the conventional Stratonovich interpretation. Here we address this dichotomy from a more generic starting point: the underdamped Langevin equation and its corresponding Fokker-Planck equation.
The valuation of currency options by fractional Brownian motion.
Shokrollahi, Foad; Kılıçman, Adem
2016-01-01
This research aims to investigate a model for pricing of currency options in which value governed by the fractional Brownian motion model (FBM). The fractional partial differential equation and some Greeks are also obtained. In addition, some properties of our pricing formula and simulation studies are presented, which demonstrate that the FBM model is easy to use. PMID:27504243
Induction generator models in dynamic simulation tools
DEFF Research Database (Denmark)
Knudsen, Hans; Akhmatov, Vladislav
1999-01-01
found to be possible to include a transient model in dynamic stability tools and, then, obtain correct results also in dynamic tools. The representation of the rotating system influences on the voltage recovery shape which is an important observation in case of windmills, where a heavy mill is connected......For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained. It is...
Some Brownian functionals and their laws
Donati-Martin, C.; Yor, M.
1997-01-01
We develop some topics about Brownian motion with a particular emphasis on the study of principal values of Brownian local times. We show some links between principal values and Doob’s $h$-transforms of Brownian motion, for nonpositive harmonic functions $h$. We also give a survey and complement some martingale approaches to Ray–Knight theorems for local times.
Fluid Dynamics Theory, Computation, and Numerical Simulation
Pozrikidis, Constantine
2009-01-01
Fluid Dynamics: Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner. The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming. This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice. There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes. Two distinguishing features of the discourse are: solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty. Matlab codes are presented and discussed for ...
Fluid dynamics theory, computation, and numerical simulation
Pozrikidis, C
2001-01-01
Fluid Dynamics Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes Two distinguishing features of the discourse are solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty Matlab codes are presented and discussed for a broad...
Zimmermann, Urs; Smallenburg, Frank; Löwen, Hartmut
2016-06-22
Using both dynamical density functional theory and particle-resolved Brownian dynamics simulations, we explore the flow of two-dimensional colloidal solids and fluids driven through a linear channel with a constriction. The flow is generated by a constant external force acting on all colloids. The initial configuration is equilibrated in the absence of flow and then the external force is switched on instantaneously. Upon starting the flow, we observe four different scenarios: a complete blockade, a monotonic decay to a constant particle flux (typical for a fluid), a damped oscillatory behaviour in the particle flux, and a long-lived stop-and-go behaviour in the flow (typical for a solid). The dynamical density functional theory describes all four situations but predicts infinitely long undamped oscillations in the flow which are always damped in the simulations. We attribute the mechanisms of the underlying stop-and-go flow to symmetry conditions on the flowing solid. Our predictions are verifiable in real-space experiments on magnetic colloidal monolayers which are driven through structured microchannels and can be exploited to steer the flow throughput in microfluidics. PMID:27116706
Monte Carlo simulation for soot dynamics
Directory of Open Access Journals (Sweden)
Zhou Kun
2012-01-01
Full Text Available A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.
Monte carlo simulation for soot dynamics
Zhou, Kun
2012-01-01
A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.
Quantum Brownian motion in a Landau level
Cobanera, E.; Kristel, P.; Morais Smith, C.
2016-06-01
Motivated by questions about the open-system dynamics of topological quantum matter, we investigated the quantum Brownian motion of an electron in a homogeneous magnetic field. When the Fermi length lF=ℏ /(vFmeff) becomes much longer than the magnetic length lB=(ℏc /e B ) 1 /2 , then the spatial coordinates X ,Y of the electron cease to commute, [X ,Y ] =i lB2 . As a consequence, localization of the electron becomes limited by Heisenberg uncertainty, and the linear bath-electron coupling becomes unconventional. Moreover, because the kinetic energy of the electron is quenched by the strong magnetic field, the electron has no energy to give to or take from the bath, and so the usual connection between frictional forces and dissipation no longer holds. These two features make quantum Brownian motion topological, in the regime lF≫lB , which is at the verge of current experimental capabilities. We model topological quantum Brownian motion in terms of an unconventional operator Langevin equation derived from first principles, and solve this equation with the aim of characterizing diffusion. While diffusion in the noncommutative plane turns out to be conventional, with the mean displacement squared being proportional to tα and α =1 , there is an exotic regime for the proportionality constant in which it is directly proportional to the friction coefficient and inversely proportional to the square of the magnetic field: in this regime, friction helps diffusion and the magnetic field suppresses all fluctuations. We also show that quantum tunneling can be completely suppressed in the noncommutative plane for suitably designed metastable potential wells, a feature that might be worth exploiting for storage and protection of quantum information.
Molecular dynamic simulation of directional crystal growth
Costa, B. V.; Coura, P. Z.; Mesquita, O. N.
1999-01-01
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach experimentally, being an important tool for further experimental and theoretical developments in the area of crystal growth.
Molecular dynamics - NMR experiments and simulations
Czech Academy of Sciences Publication Activity Database
Dračínský, Martin; Hodgkinson, P.; Kessler, Jiří; Bouř, Petr
Brno : Masaryk University Press, 2015 - (Sklenář, V.). s. 277-278 ISBN 978-80-210-7890-1. [EUROMAR 2015. 05.07.2015-10.07.2015, Praha] Institutional support: RVO:61388963 Keywords : molecular dynamics * NMR spectroscopy * MD simulations Subject RIV: CF - Physical ; Theoretical Chemistry
Object Oriented Modelling and Dynamical Simulation
DEFF Research Database (Denmark)
Wagner, Falko Jens; Poulsen, Mikael Zebbelin
1998-01-01
This report with appendix describes the work done in master project at DTU.The goal of the project was to develop a concept for simulation of dynamical systems based on object oriented methods.The result was a library of C++-classes, for use when both building componentbased models and when...
Dynamic simulation of a reverse Brayton refrigerator
Energy Technology Data Exchange (ETDEWEB)
Peng, N.; Xiong, L. Y.; Dong, B.; Liu, L. Q. [State Key Laboratory of Technologies in Space Cryogenic Propellants, Technical Institute of Physics and Chemistry, CAS, Beijing, 100190 (China); Lei, L. L.; Tang, J. C. [State Key Laboratory of Technologies in Space Cryogenic Propellants, Technical Institute of Physics and Chemistry, CAS, Beijing, 100190 China and Graduate University of Chinese Academy of Sciences, Beijing, 100190 (China)
2014-01-29
A test refrigerator based on the modified Reverse Brayton cycle has been developed in the Chinese Academy of Sciences recently. To study the behaviors of this test refrigerator, a dynamic simulation has been carried out. The numerical model comprises the typical components of the test refrigerator: compressor, valves, heat exchangers, expander and heater. This simulator is based on the oriented-object approach and each component is represented by a set of differential and algebraic equations. The control system of the test refrigerator is also simulated, which can be used to optimize the control strategies. This paper describes all the models and shows the simulation results. Comparisons between simulation results and experimental data are also presented. Experimental validation on the test refrigerator gives satisfactory results.
Dynamic modeling and simulation of wind turbines
International Nuclear Information System (INIS)
Using wind energy for generating electricity in wind turbines is a good way for using renewable energies. It can also help to protect the environment. The main objective of this paper is dynamic modeling by energy method and simulation of a wind turbine aided by computer. In this paper, the equations of motion are extracted for simulating the system of wind turbine and then the behavior of the system become obvious by solving the equations. The turbine is considered with three blade rotor in wind direction, induced generator that is connected to the network and constant revolution for simulation of wind turbine. Every part of the wind turbine should be simulated for simulation of wind turbine. The main parts are blades, gearbox, shafts and generator
Dynamic simulation of a reverse Brayton refrigerator
International Nuclear Information System (INIS)
A test refrigerator based on the modified Reverse Brayton cycle has been developed in the Chinese Academy of Sciences recently. To study the behaviors of this test refrigerator, a dynamic simulation has been carried out. The numerical model comprises the typical components of the test refrigerator: compressor, valves, heat exchangers, expander and heater. This simulator is based on the oriented-object approach and each component is represented by a set of differential and algebraic equations. The control system of the test refrigerator is also simulated, which can be used to optimize the control strategies. This paper describes all the models and shows the simulation results. Comparisons between simulation results and experimental data are also presented. Experimental validation on the test refrigerator gives satisfactory results
Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow
Archereau, Aurelien Y M; Willmott, Geoff R
2016-01-01
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.
Computer simulation of confined liquid crystal dynamics
Webster, R E
2001-01-01
are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results...
Probing Cellular Dynamics with Mesoscopic Simulations
DEFF Research Database (Denmark)
Shillcock, Julian C.
2010-01-01
Cellular processes span a huge range of length and time scales from the molecular to the near-macroscopic. Understanding how effects on one scale influence, and are themselves influenced by, those on lower and higher scales is a critical issue for the construction of models in Systems Biology....... Advances in computing hardware and software now allow explicit simulation of some aspects of cellular dynamics close to the molecular scale. Vesicle fusion is one example of such a process. Experiments, however, typically probe cellular behavior from the molecular scale up to microns. Standard particle...... soon be coupled to Mass Action models allowing the parameters in such models to be continuously tuned according to the finer resolution simulation. This will help realize the goal of a computational cellular simulation that is able to capture the dynamics of membrane-associated processes such as...
Perturbative theory for Brownian vortexes.
Moyses, Henrique W; Bauer, Ross O; Grosberg, Alexander Y; Grier, David G
2015-06-01
Brownian vortexes are stochastic machines that use static nonconservative force fields to bias random thermal fluctuations into steadily circulating currents. The archetype for this class of systems is a colloidal sphere in an optical tweezer. Trapped near the focus of a strongly converging beam of light, the particle is displaced by random thermal kicks into the nonconservative part of the optical force field arising from radiation pressure, which then biases its diffusion. Assuming the particle remains localized within the trap, its time-averaged trajectory traces out a toroidal vortex. Unlike trivial Brownian vortexes, such as the biased Brownian pendulum, which circulate preferentially in the direction of the bias, the general Brownian vortex can change direction and even topology in response to temperature changes. Here we introduce a theory based on a perturbative expansion of the Fokker-Planck equation for weak nonconservative driving. The first-order solution takes the form of a modified Boltzmann relation and accounts for the rich phenomenology observed in experiments on micrometer-scale colloidal spheres in optical tweezers. PMID:26172698
Atomic dynamics of alumina melt: A molecular dynamics simulation study
Directory of Open Access Journals (Sweden)
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
Engineering dynamics from the Lagrangian to simulation
Gans, Roger F
2013-01-01
This engineering dynamics textbook is aimed at beginning graduate students in mechanical engineering and other related engineering disciplines who need training in dynamics as applied to engineering mechanisms. It introduces the formal mathematical development of Lagrangian mechanics (and its corollaries), while solving numerous engineering applications. The author’s goal is to instill an understanding of the basic physics required for engineering dynamics, while providing a recipe (algorithm) for the simulation of engineering mechanisms such as robots. The book is reasonably self-contained so that the practicing engineer interested in this area can also make use of it. This book is made accessible to the widest possible audience by numerous, solved examples and diagrams that apply the principles to real engineering applications. • Provides an applied textbook for intermediate/advanced engineering dynamics courses; • Discusses Lagrangian mechanics in the context of numerous engineering applications...
Institute of Scientific and Technical Information of China (English)
秦天奇; 王飞; 杨博; 罗懋康
2015-01-01
Based on the theory of fractional integration, direct transport behaviors of coupled Brownian motors with feedback control in viscoelastic media are investigated. The mathematical model of fractional overdamped coupled Brownian motors is established by adopting the power function as damping kernel function of general Langevin equation due to the power-law memory characteristics of cytosol in biological cells. Numerical solution is observed by fractional difference method and the influence of model parameters on cooperative direct transport of the coupled Brownian motors is discussed in detail by numerical simulation. The research shows that the memory of the fractional dynamical system can affect the direct transport phenomenon of the coupled Brownian motors through changing the on-off switching frequency of the ratchet potential with feedback control. To be more specific, in a proper range of the fractional order, the memory of the dynamical system can increase the on-off switching frequency of the ratchet potential, which can lead to the velocity increase of the direct transport. Furthermore, in the case of small fractional order, since the coupled Brownian motors move under the competition between the damping force with memory and the potential force with feedback control, the resultant force exerted on the coupled particles is always positive when the ratchet potential with feedback control is on although the fractional damping force is large, which leads to the result that the coupled Brownian motors move in the positive direction in the mass. On the contrary, in the case of large fractional order, the on-off switching frequency of potential with feedback control becomes small, as a result of which the main influential factor of the direct transport becomes the potential depth. Therefore the coupled Brownian motors are more likely to stay in the potential wells for a long time because the probability that describes the possibility that the coupled Brownian
Simulation studies using multibody dynamics code DART
Keat, James E.
1989-01-01
DART is a multibody dynamics code developed by Photon Research Associates for the Air Force Astronautics Laboratory (AFAL). The code is intended primarily to simulate the dynamics of large space structures, particularly during the deployment phase of their missions. DART integrates nonlinear equations of motion numerically. The number of bodies in the system being simulated is arbitrary. The bodies' interconnection joints can have an arbitrary number of degrees of freedom between 0 and 6. Motions across the joints can be large. Provision for simulating on-board control systems is provided. Conservation of energy and momentum, when applicable, are used to evaluate DART's performance. After a brief description of DART, studies made to test the program prior to its delivery to AFAL are described. The first is a large angle reorientating of a flexible spacecraft consisting of a rigid central hub and four flexible booms. Reorientation was accomplished by a single-cycle sine wave shape torque input. In the second study, an appendage, mounted on a spacecraft, was slewed through a large angle. Four closed-loop control systems provided control of this appendage and of the spacecraft's attitude. The third study simulated the deployment of the rim of a bicycle wheel configuration large space structure. This system contained 18 bodies. An interesting and unexpected feature of the dynamics was a pulsing phenomena experienced by the stays whole playout was used to control the deployment. A short description of the current status of DART is given.
Müller, Kei W.; Meier, Christoph; Wall, Wolfgang A.
2015-12-01
Networks of crosslinked biopolymer filaments such as the cytoskeleton are the subject of intense research. Oftentimes, mechanics on the scale of single monomers (∼ 5 nm) govern the mechanics of the entire network (∼ 10 μm). Until now, one either resolved the small scales and lost the big (network) picture or focused on mechanics above the single-filament scale and neglected the molecular architecture. Therefore, the study of network mechanics influenced by the entire spectrum of relevant length scales has been infeasible so far. We propose a method that reconciles both small and large length scales without the otherwise inevitable loss in either numerical efficiency or geometrical (molecular) detail. Both explicitly modeled species, filaments and their crosslinkers, are discretized with geometrically exact beam finite elements of Simo-Reissner type. Through specific coupling conditions between the elements of the two species, mechanical joints can be established anywhere along a beam's centerline, enabling arbitrary densities of chemical binding sites. These binding sites can be oriented to model the monomeric architecture of polymers. First, we carefully discuss the method and then demonstrate its capabilities by means of a series of numerical examples.
Cleuren, Bart; Van den Broeck, Christian
2007-01-01
An asymmetric object, undergoing dissipative collisions with surrounding particles, acquires a nonzero average velocity. The latter is calculated analytically by an expansion of the Boltzmann equation and the result is compared with Monte Carlo simulations. Copyright (c) EPLA, 2007
Hydrogen Bond in Liquid Water as a Brownian Oscillator
Woutersen, Sander; Bakker, Huib J.
1999-09-01
We present the first experimental observation of a vibrational dynamic Stokes shift. This dynamic Stokes shift is observed in a femtosecond pump-probe study on the OH-stretch vibration of HDO dissolved in D2O. We find that the Stokes shift has a value of approximately 70 cm-1 and occurs with a time constant of approximately 500 femtoseconds. The measurements can be accurately described by modeling the hydrogen bond in liquid water as a Brownian oscillator.
Simulation of Boiling Water Reactor dynamics
International Nuclear Information System (INIS)
This master thesis describes a mathematical model of a boiling water reactor and address the dynamic behaviour of the neutron kinetics, boilding dynamics and pressur stability. The simulation have been done using the SIMNON-program. The meaning were that the result from this work possibly would be adjust to supervision methods suitable for application in computer systems. This master thesis in automatic control has been done at the Department of Automatic Control, Lund Institute of Technology. The initiative to the work came from Sydkraft AB. (author)
Dynamic simulation of the mastication muscles
Weingaertner, Tim; Albrecht, Jochen
1998-05-01
The purpose of a simulated operation system in craniofacial surgery is to evaluate and visualize the results of operations on the overall facial shape of the patient and on the functionality of his jaw. This paper presents the analyzation of muscle movements in the mastication system by applying real jaw movements to the simulation. With this method an accurate modeling of the mastication muscles can be performed which is a prerequisite for a realistic simulation and precise intra- operative registration. According to this results a large- scale musculoskeletal model of the mastication system is generated including kinematic and dynamic parameters. By integrating distance sensors in the simulation of a segmented CT (computer tomograph) image of the maxilla and mandible the motions of the masticatory muscles during different kinds of jaw movements have been analyzed. The data for this motions have been recorded by a commercial system (CONDYLOCOMP LR3) on a test person and transformed to the graphical simulation system. This method for the first time allows to observe the dynamics of the mastication muscles and their different parameters like muscle length ratio and velocity. The integration of a kinematic model for the jaw movement makes it possible to analyze non traced movements.
Dynamic Simulation of a Helium Liquefier
International Nuclear Information System (INIS)
Dynamic behavior of a helium liquefier has been studied in detail with a Cryogenic Process REal-time SimulaTor (C-PREST) at the National Institute for Fusion Science (NIFS). The C-PREST is being developed to integrate large-scale helium cryogenic plant design, operation and maintenance for optimum process establishment. As a first step of simulations of cooldown to 4.5 K with the helium liquefier model is conducted, which provides a plant-process validation platform. The helium liquefier consists of seven heat exchangers, a liquid-nitrogen (LN2) precooler, two expansion turbines and a liquid-helium (LHe) reservoir. Process simulations are fulfilled with sequence programs, which were implemented with C-PREST based on an existing liquefier operation. The interactions of a JT valve, a JT-bypass valve and a reservoir-return valve have been dynamically simulated. The paper discusses various aspects of refrigeration process simulation, including its difficulties such as a balance between complexity of the adopted models and CPU time
Parallelization of quantum molecular dynamics simulation code
International Nuclear Information System (INIS)
A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)
Description of the grout system dynamic simulation
International Nuclear Information System (INIS)
The grout system dynamic computer simulation was created to allow investigation of the ability of the grouting system to meet established milestones, for various assumed system configurations and parameters. The simulation simulates the movement of tank waste through the system versus time, from initial storage tanks, through feed tanks and the grout plant, then finally to a grout vault. The simulation properly accounts for the following (1) time required to perform various actions or processes, (2) delays involved in gaining regulatory approval, (3) random system component failures, (4) limitations on equipment capacities, (5) available parallel components, and (6) different possible strategies for vault filling. The user is allowed to set a variety of system parameters for each simulation run. Currently, the output of a run primarily consists of a plot of projected grouting campaigns completed versus time, for comparison with milestones. Other outputs involving any model component can also be quickly created or deleted as desired. In particular, sensitivity runs where the effect of varying a model parameter (flow rates, delay times, number of feed tanks available, etc.) on the ability of the system to meet milestones can be made easily. The grout system simulation was implemented using the ITHINK* simulation language for Macintosh** computers
Molecular dynamics simulation for modelling plasma spectroscopy
Talin, B; Calisti, A; Gigosos, M A; González, M A; Gaztelurrutia, T R; Dufty, J W
2003-01-01
The ion-electron coupling properties for an ion impurity in an electron gas and for a two-component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely motivated by the study of radiator dipole relaxation in plasmas which makes a real link between models and experiments. Current radiative property models for plasmas include single electron collisions neglecting charge-charge correlations within the classical quasi-particle approach commonly used in this field. The dipole relaxation simulation based on electron-ion molecular dynamics proposed here will provide a means to benchmark and improve model developments. Benefiting from a detailed study of a single ion embedded in an electron plasma, the challenging two-component ion-electron molecular dynamics simulations are proved accurate. They open new possibilities of obtaining reference lineshape data.
Simulation of Abrasive Machining Using Molecular Dynamics
Oluwajobi, Akinjide O.; Chen, Xun
2009-01-01
The development of ultra–precision processes which can achieve excellent surface finish and tolerance at nanometre level is now a critical requirement for many applications in medical, electronics and energy industry. Presently, it is very difficult to observe the diverse microscopic physical phenomena occurring in nanometric machining through experiments. The use of Molecular Dynamics (MD) simulation has proved to be an effective tool for the prediction and the analysis ...
Parallel beam dynamics simulation of linear accelerators
Qiang, Ji; Ryne, Robert D.
2002-01-01
In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity b...
Molecular dynamics simulation of expanding infinite matter
International Nuclear Information System (INIS)
Multi-fragmentation occurred in an expanding infinite system is studied by using molecular dynamics simulation. To evaluate the secondary decay effect, the time evolution of expanding system is proceeded till all fragments are stabilized completely. The fragment mass distribution from the expansion is compared with a percolation model and the cause of the exponential shape is clarified. The cause of small critical temperature is also discussed. (author)
Schwinger model simulations with dynamical overlap fermions
Bietenholz, Wolfgang; Shcheredin, Stanislav; Volkholz, Jan
2007-01-01
We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate Sigma vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the l...
Temperature Dependent Molecular Dynamic Simulation of Friction
Dias, R A; Coura, P Z; Costa, B V
2006-01-01
In this work we present a molecular dynamics simulation of a FFM experiment. The tip-sample interaction is studied by varying the normal force in the tip and the temperature of the surface. The friction force, cA, at zero load and the friction coefficient, $\\mu$, were obtained. Our results strongly support the idea that the effective contact area, A, decreases with increasing temperature and the friction coefficient presents a clear signature of the premelting process of the surface.
Dislocation dynamics simulations in a cylinder
Energy Technology Data Exchange (ETDEWEB)
Weinberger, Christopher R; Aubry, Sylvie; Cai, Wei [Department of Mechanical Engineering, Stanford University, Stanford, CA 94305-4040 (United States); Lee, Seok-Woo, E-mail: cweinber@stanford.edu, E-mail: caiwei@stanford.edu [Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305-4034 (United States)
2009-07-15
In this work we describe how to perform dislocation dynamics simulations in a cylindrical geometry. An algorithm for computing the image stress is given in detail including methods for handling the singularity. Additional remesh rules address the problems of the cylindrical geometry and the required self consistency with mobility laws. Numerical studies benchmark the accuracy of the algorithms and the importance of handling the singularity correctly.
Simulating granular flow with molecular dynamics
Ristow, Gerald
1992-01-01
We investigate by means of Molecular Dynamics simulations an assembly of spheres to model a granular medium flowing from an upper rectangular chamber through a hole into a lower chamber. Two different two dimensional models are discussed one of them including rotations of the individual spheres. The outflow properties are investigated and compared to experimental data. The qualitative agreement suggests that our models contain the necessary ingredients to describe the outflow properties of gr...
Simulation of counterflow pedestrian dynamics using spheropolygons
Alonso-Marroquín, Fernando; Busch, Jonathan; Chiew, Coraline; Lozano, Celia; Ramírez-Gómez, Álvaro
2014-12-01
Pedestrian dynamic models are typically designed for comfortable walking or slightly congested conditions and typically use a single disk or combination of three disks for the shape of a pedestrian. Under crowd conditions, a more accurate pedestrian shape has advantages over the traditional single or three-disks model. We developed a method for simulating pedestrian dynamics in a large dense crowd of spheropolygons adapted to the cross section of the chest and arms of a pedestrian. Our numerical model calculates pedestrian motion from Newton's second law, taking into account viscoelastic contact forces, contact friction, and ground-reaction forces. Ground-reaction torque was taken to arise solely from the pedestrians' orientation toward their preferred destination. Simulations of counterflow pedestrians dynamics in corridors were used to gain insight into a tragic incident at the Madrid Arena pavilion in Spain, where five girls were crushed to death. The incident took place at a Halloween Celebration in 2012, in a long, densely crowded hallway used as entrance and exit at the same time. Our simulations reconstruct the mechanism of clogging in the hallway. The hypothetical case of a total evacuation order was also investigated. The results highlights the importance of the pedestrians' density and the effect of counterflow in the onset of avalanches and clogging and provides an estimation of the number of injuries based on a calculation of the contact-force network between the pedestrians.
Electronic continuum model for molecular dynamics simulations.
Leontyev, I V; Stuchebrukhov, A A
2009-02-28
A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627
Generator dynamics in aeroelastic analysis and simulations
DEFF Research Database (Denmark)
Larsen, Torben J.; Hansen, Morten Hartvig; Iov, F.
2003-01-01
of the first order terms in the model as well as the influence on drive train eigenfrequencies and damping has been investigated. Load response during timesimulation of wind turbine response have been compared to simulations with a traditional static generator model based entirely on the slip angle....... A 2 MW turbine has been modelled in the aeroelastic code HAWC. When using the new dynamic generator modelthere is an interesting coupling between the generator dynamics and a global turbine vibration mode at 4.5 Hz, which only occurs when a dynamic formulation of the generator equations is applied....... This frequency can especially be seen in the electricalpower of the generator and the rotational speed of the generator, but also as torque variations in the drive train....
Adaptive wavelet simulation of global ocean dynamics
Directory of Open Access Journals (Sweden)
N. K.-R. Kevlahan
2015-07-01
Full Text Available In order to easily enforce solid-wall boundary conditions in the presence of complex coastlines, we propose a new mass and energy conserving Brinkman penalization for the rotating shallow water equations. This penalization does not lead to higher wave speeds in the solid region. The error estimates for the penalization are derived analytically and verified numerically for linearized one dimensional equations. The penalization is implemented in a conservative dynamically adaptive wavelet method for the rotating shallow water equations on the sphere with bathymetry and coastline data from NOAA's ETOPO1 database. This code could form the dynamical core for a future global ocean model. The potential of the dynamically adaptive ocean model is illustrated by using it to simulate the 2004 Indonesian tsunami and wind-driven gyres.
Dynamic simulation analyzes expanded refinery steam system
Energy Technology Data Exchange (ETDEWEB)
Gandhi, S.L.; Graham, J.; Duffield, M.A.; Cortes, R.M. [M.W. Kellogg Co., Houston, TX (United States)
1995-11-01
There is a rising demand for more-stable process operations with increasing facility modernization and automation. This requires steam system controls that provide effective and stable responses to operational disturbances. Today it is possible to use dynamic simulation analysis for designing steam systems. The main objectives were to: develop a high-fidelity dynamic simulation model of the steam system and its associated controls; develop dynamic system responses to major plant disturbances; and assist in designing new control strategies and modifying existing controls to minimize the impact of plant upsets on system performance. The steam system for this project included two power plant supplying steam and power and a steam pipe network comprising three levels of steam with stream flows to and from process units spread over several square kilometers. Whether the steam system and its controls would respond effectively to major operational upsets, such as boiler, steam turbogenerator or process gas compressor trips, or a steep increase in steam demand, can only be determined from evaluating dynamic responses to these incidents. The model consisted of about 5,000 equations, 1,000 parameters and data items, and was used for evaluating steam system responses to various operational upset scenarios. The responses were used to identify limitations of the as designed control system. The model also proved to be an effective tool for verifying adequacy of the proposed recommendations. These included modifications to control valve letdown stations, steam turbogenerator governor controls and the boiler master-pressure controller.
SIMULATION OF INTERLINE DYNAMIC VOLTAGE RESTORER
Directory of Open Access Journals (Sweden)
J.Singaravelan
2011-08-01
Full Text Available This paper presents a new approach for the dynamic control of a current source inverter (CSI using Super Conductive Magnetic energy storage (SMES based Interline DVR. The dynamic voltage restorer (DVR provides a technically advanced and economical solution to voltage-sag problem. As the voltage-restoration process involves the real-power injection into the distribution system, the capability ofa DVR, especially for compensating long-duration voltage sags, it depends on the energy storage capacity of the DVR. The interline DVR proposed in this paper provides a way to replenish Dc-link energy storage dynamically. The IDVR consists of several DVRs connected to different distribution feeders in the power system. The DVRs in the IDVR system shares the common energy storage. When one of the DVRcompensates for voltage sag appearing in that feeder, the other DVRs replenish the energy in the common dc-link dynamically. Thus, one DVR in the IDVR system works in voltage-sag compensation mode whilethe other DVRs in the IDVR system operate in power-flow control mode. The proposed topology is simulated using Matlab/Simulink and total IDVR system is simulated using Matlab/Simulink.
Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations
Byutner, Oleksiy; Smith, Grant
2001-03-01
In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.
A molecular dynamics simulation code ISIS
International Nuclear Information System (INIS)
Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)
Dynamic simulator for PEFC propulsion plant
Energy Technology Data Exchange (ETDEWEB)
Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao [Mitsui Engineering & Shipbuilding Co., Ltd., Tokyo (Japan)] [and others
1996-12-31
This report covers part of a joint study on a PEFC propulsion system for surface ships, summarized in a presentation to this Seminar, entitled {open_quote}Study on a Polymer Electrolyte Fuel Cell (PEFC) Propulsion System for Surface Ships{close_quotes}, and which envisages application to a 1,500 DWT cargo vessel. The work presented here focuses on a simulation study on PEFC propulsion plant performance, and particularly on the system response to changes in load. Using a dynamic simulator composed of system components including fuel cell, various simulations were executed, to examine the performance of the system as a whole and of the individual system components under quick and large load changes such as occasioned by maneuvering operations and by racing when the propeller emerges above water in heavy sea.
Efficiency of Brownian heat engines.
Derényi, I; Astumian, R D
1999-06-01
We study the efficiency of one-dimensional thermally driven Brownian ratchets or heat engines. We identify and compare the three basic setups characterized by the type of the connection between the Brownian particle and the two heat reservoirs: (i) simultaneous, (ii) alternating in time, and (iii) position dependent. We make a clear distinction between the heat flow via the kinetic and the potential energy of the particle, and show that the former is always irreversible and it is only the third setup where the latter is reversible when the engine works quasistatically. We also show that in the third setup the heat flow via the kinetic energy can be reduced arbitrarily, proving that even for microscopic heat engines there is no fundamental limit of the efficiency lower than that of a Carnot cycle. PMID:11969723
Brownian motion and stochastic calculus
Karatzas, Ioannis
1998-01-01
This book is designed as a text for graduate courses in stochastic processes. It is written for readers familiar with measure-theoretic probability and discrete-time processes who wish to explore stochastic processes in continuous time. The vehicle chosen for this exposition is Brownian motion, which is presented as the canonical example of both a martingale and a Markov process with continuous paths. In this context, the theory of stochastic integration and stochastic calculus is developed. The power of this calculus is illustrated by results concerning representations of martingales and change of measure on Wiener space, and these in turn permit a presentation of recent advances in financial economics (option pricing and consumption/investment optimization). This book contains a detailed discussion of weak and strong solutions of stochastic differential equations and a study of local time for semimartingales, with special emphasis on the theory of Brownian local time. The text is complemented by a large num...
Hänggi, Peter; Marchesoni, Fabio
2005-01-01
In the year 1905 Albert Einstein published four papers that raised him to a giant in the history of science of all times. These works encompass the photon hypothesis (for which he obtained the Nobel prize in 1921), his first two papers on (special) relativity theory and, of course, his first paper on Brownian motion, entitled "\\"Uber die von der molekularkinetischen Theorie der W\\"arme geforderte Bewegung von in ruhenden Fl\\"ussigkeiten suspendierten Teilchen'' (submitted on May 11, 1905). Th...
Kingman's coalescent and Brownian motion
Berestycki, J.; Berestycki, N
2009-01-01
We describe a simple construction of Kingman's coalescent in terms of a Brownian excursion. This construction is closely related to, and sheds some new light on, earlier work by Aldous and Warren. Our approach also yields some new results: for instance, we obtain the full multifractal spectrum of Kingman's coalescent. This complements earlier work on Beta-coalescents by the authors and Schweinsberg. Surprisingly, the thick part of the spectrum is not obtained by taking the limit as $\\alpha \\t...
Brownian ratchets and Parrondo's games
Harmer, Gregory P.; Abbott, Derek; Taylor, Peter G.; Parrondo, Juan M. R.
2001-09-01
Parrondo's games present an apparently paradoxical situation where individually losing games can be combined to win. In this article we analyze the case of two coin tossing games. Game B is played with two biased coins and has state-dependent rules based on the player's current capital. Game B can exhibit detailed balance or even negative drift (i.e., loss), depending on the chosen parameters. Game A is played with a single biased coin that produces a loss or negative drift in capital. However, a winning expectation is achieved by randomly mixing A and B. One possible interpretation pictures game A as a source of "noise" that is rectified by game B to produce overall positive drift—as in a Brownian ratchet. Game B has a state-dependent rule that favors a losing coin, but when this state dependence is broken up by the noise introduced by game A, a winning coin is favored. In this article we find the parameter space in which the paradoxical effect occurs and carry out a winning rate analysis. The significance of Parrondo's games is that they are physically motivated and were originally derived by considering a Brownian ratchet—the combination of the games can be therefore considered as a discrete-time Brownian ratchet. We postulate the use of games of this type as a toy model for a number of physical and biological processes and raise a number of open questions for future research.
INCORPORATING DYNAMIC 3D SIMULATION INTO PRA
Energy Technology Data Exchange (ETDEWEB)
Steven R Prescott; Curtis Smith
2011-07-01
provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.
International Nuclear Information System (INIS)
The extinction coefficient of atmospheric aerosol particles influences the earth’s radiation balance directly or indirectly, and it can be determined by the scattering and absorption characteristics of aerosol particles. The problem of estimating the change of extinction coefficient due to time evolution of bimodal particle size distribution is studied, and two improved methods for calculating the Brownian coagulation coefficient and the condensation growth rate are proposed, respectively. Through the improved method based on Otto kernel, the Brownian coagulation coefficient can be expressed simply in powers of particle volume for the entire particle size regime based on the fitted polynomials of the mean enhancement function. Meanwhile, the improved method based on Fuchs–Sutugin kernel is developed to obtain the condensation growth rate for the entire particle size regime. And then, the change of the overall extinction coefficient of bimodal distributions undergoing Brownian coagulation and condensation can be estimated comprehensively for the entire particle size regime. Simulation experiments indicate that the extinction coefficients obtained with the improved methods coincide fairly well with the true values, which provide a simple, reliable, and general method to estimate the change of extinction coefficient for the entire particle size regime during the bimodal particle dynamic processes.
Maximum of a Fractional Brownian Motion: Analytic Results from Perturbation Theory.
Delorme, Mathieu; Wiese, Kay Jörg
2015-11-20
Fractional Brownian motion is a non-Markovian Gaussian process X_{t}, indexed by the Hurst exponent H. It generalizes standard Brownian motion (corresponding to H=1/2). We study the probability distribution of the maximum m of the process and the time t_{max} at which the maximum is reached. They are encoded in a path integral, which we evaluate perturbatively around a Brownian, setting H=1/2+ϵ. This allows us to derive analytic results beyond the scaling exponents. Extensive numerical simulations for different values of H test these analytical predictions and show excellent agreement, even for large ϵ. PMID:26636835
Communication: Memory effects and active Brownian diffusion
International Nuclear Information System (INIS)
A self-propelled artificial microswimmer is often modeled as a ballistic Brownian particle moving with constant speed aligned along one of its axis, but changing direction due to random collisions with the environment. Similarly to thermal noise, its angular randomization is described as a memoryless stochastic process. Here, we speculate that finite-time correlations in the orientational dynamics can affect the swimmer’s diffusivity. To this purpose, we propose and solve two alternative models. In the first one, we simply assume that the environmental fluctuations governing the swimmer’s propulsion are exponentially correlated in time, whereas in the second one, we account for possible damped fluctuations of the propulsion velocity around the swimmer’s axis. The corresponding swimmer’s diffusion constants are predicted to get, respectively, enhanced or suppressed upon increasing the model memory time. Possible consequences of this effect on the interpretation of the experimental data are discussed
Communication: Memory effects and active Brownian diffusion.
Ghosh, Pulak K; Li, Yunyun; Marchegiani, Giampiero; Marchesoni, Fabio
2015-12-01
A self-propelled artificial microswimmer is often modeled as a ballistic Brownian particle moving with constant speed aligned along one of its axis, but changing direction due to random collisions with the environment. Similarly to thermal noise, its angular randomization is described as a memoryless stochastic process. Here, we speculate that finite-time correlations in the orientational dynamics can affect the swimmer's diffusivity. To this purpose, we propose and solve two alternative models. In the first one, we simply assume that the environmental fluctuations governing the swimmer's propulsion are exponentially correlated in time, whereas in the second one, we account for possible damped fluctuations of the propulsion velocity around the swimmer's axis. The corresponding swimmer's diffusion constants are predicted to get, respectively, enhanced or suppressed upon increasing the model memory time. Possible consequences of this effect on the interpretation of the experimental data are discussed. PMID:26646861
Communication: Memory effects and active Brownian diffusion
Energy Technology Data Exchange (ETDEWEB)
Ghosh, Pulak K. [Department of Chemistry, Presidency University, Kolkata 700073 (India); Li, Yunyun, E-mail: yunyunli@tongji.edu.cn [Center for Phononics and Thermal Energy Science, Tongji University, Shanghai 200092 (China); Marchegiani, Giampiero [Dipartimento di Fisica, Università di Camerino, I-62032 Camerino (Italy); Marchesoni, Fabio [Center for Phononics and Thermal Energy Science, Tongji University, Shanghai 200092 (China); Dipartimento di Fisica, Università di Camerino, I-62032 Camerino (Italy)
2015-12-07
A self-propelled artificial microswimmer is often modeled as a ballistic Brownian particle moving with constant speed aligned along one of its axis, but changing direction due to random collisions with the environment. Similarly to thermal noise, its angular randomization is described as a memoryless stochastic process. Here, we speculate that finite-time correlations in the orientational dynamics can affect the swimmer’s diffusivity. To this purpose, we propose and solve two alternative models. In the first one, we simply assume that the environmental fluctuations governing the swimmer’s propulsion are exponentially correlated in time, whereas in the second one, we account for possible damped fluctuations of the propulsion velocity around the swimmer’s axis. The corresponding swimmer’s diffusion constants are predicted to get, respectively, enhanced or suppressed upon increasing the model memory time. Possible consequences of this effect on the interpretation of the experimental data are discussed.
Extreme fluctuations of active Brownian motion
Pietzonka, Patrick; Kleinbeck, Kevin; Seifert, Udo
2016-05-01
In active Brownian motion, an internal propulsion mechanism interacts with translational and rotational thermal noise and other internal fluctuations to produce directed motion. We derive the distribution of its extreme fluctuations and identify its universal properties using large deviation theory. The limits of slow and fast internal dynamics give rise to a kink-like and parabolic behavior of the corresponding rate functions, respectively. For dipolar Janus particles in two- and three-dimensions interacting with a field, we predict a novel symmetry akin to, but different from, the one related to entropy production. Measurements of these extreme fluctuations could thus be used to infer properties of the underlying, often hidden, network of states.
Evaluating changes of writhe in computer simulations of supercoiled DNA
Vries, de R.J.
2005-01-01
We compute changes in the writhe of a polygonal space curve when one of the vertices is displaced. The resulting expressions can be used in simulations of supercoiled DNA. For Brownian dynamics simulations, the expressions can be used to eliminate the explicit twisting degree of freedom. For Monte C
Computer simulation of confined liquid crystal dynamics
International Nuclear Information System (INIS)
Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. (author)
Information field dynamics for simulation scheme construction
Enßlin, Torsten A
2012-01-01
Information field dynamics (IFD) is introduced here as a framework to derive numerical schemes for the simulation of physical and other fields. Any simulation scheme updates a discretized field representation, the data in a computer's memory, for the next time step according to a discretized, approximate representation of the underlying field dynamics. Assumptions about the continuum field behavior on sub-grid scales are reflected in these rules, e.g. the field might be assumed to be constant within a grid cell, or to be some weighted average of neighboring data points, and the like. In contrast to such parametrized sub-grid field structures, IFD constructs non-parametric sub-grid field configurations from the combination of the data, representing constraints on possible field configurations, and prior assumptions on the sub-grid field statistics. Each of these field configurations can formally be evolved to a later moment since any differential operator of the dynamics can act on fields living in continuous ...
Hybrid scheme for Brownian semistationary processes
DEFF Research Database (Denmark)
Bennedsen, Mikkel; Lunde, Asger; Pakkanen, Mikko S.
We introduce a simulation scheme for Brownian semistationary processes, which is based on discretizing the stochastic integral representation of the process in the time domain. We assume that the kernel function of the process is regularly varying at zero. The novel feature of the scheme is to...... approximate the kernel function by a power function near zero and by a step function elsewhere. The resulting approximation of the process is a combination of Wiener integrals of the power function and a Riemann sum, which is why we call this method a hybrid scheme. Our main theoretical result describes the...... asymptotics of the mean square error of the hybrid scheme and we observe that the scheme leads to a substantial improvement of accuracy compared to the ordinary forward Riemann-sum scheme, while having the same computational complexity. We exemplify the use of the hybrid scheme by two numerical experiments...
Dynamic Simulation of Chemical Kinetics in Microcontroller
Directory of Open Access Journals (Sweden)
Renato Dutra Pereira Filho
2014-12-01
Full Text Available Arduino boards are interesting computational tools due to low cost and power consumption, as well as I/O ports, both analogs and digitals. Yet, small memory and clock frequency with truncation errors may disrupt numerical processing. This study aimed to design and evaluate the performance of a dynamic simulation based on ODEs in the Arduino, with three evaluated microprocessors; ATMEGA 328P and 2560, both 8 bits, and SAM3X8E Atmel ARM CORTEX – 32 bits. The study case was a batch reactor dynamic simulation. The Runge-Kutta 4th order algorithm was written in C++ and compiled for EPROM utilization. The output was a 115000bit/s serial connection. Processing time was almost identical for 8 bits architectures, while 32 bits was 25% faster. Without the serial connection the 8 bits architectures were 16 times faster and the 32 bits was 42 times faster. Error truncation was similar, since the floating points are done through software. The Arduino platform, despite its modest hardware, allows simple chemical systems simulation
Operator Fractional Brownian Motion and Martingale Differences
Directory of Open Access Journals (Sweden)
Hongshuai Dai
2014-01-01
Full Text Available It is well known that martingale difference sequences are very useful in applications and theory. On the other hand, the operator fractional Brownian motion as an extension of the well-known fractional Brownian motion also plays an important role in both applications and theory. In this paper, we study the relation between them. We construct an approximation sequence of operator fractional Brownian motion based on a martingale difference sequence.
Effect of solvent on directional drift in Brownian motion of particle/molecule with broken symmetry
Kong, FanDong; Sheng, Nan; Wan, RongZheng; Hu, GuoHui; Fang, HaiPing
2016-08-01
The directional drifting of particles/molecules with broken symmetry has received increasing attention. Through molecular dynamics simulations, we investigate the effects of various solvents on the time-dependent directional drifting of a particle with broken symmetry. Our simulations show that the distance of directional drift of the asymmetrical particle is reduced while the ratio of the drift to the mean displacement of the particle is enhanced with increasing mass, size, and interaction strength of the solvent atoms in a short time range. Among the parameters considered, solvent atom size is a particularly influential factor for enhancing the directional drift of asymmetrical particles, while the effects of the interaction strength and the mass of the solvent atoms are relatively weaker. These findings are of great importance to the understanding and control of the Brownian motion of particles in various physical, chemical, and biological processes within finite time spans.
100 years of Einstein's theory of Brownian motion: from pollen grains to protein trains
Chowdhury, Debashish
2005-01-01
Experimental verification of the theoretical predictions made by Albert Einstein in his paper, published in 1905, on the molecular mechanisms of Brownian motion established the existence of atoms. In the last 100 years discoveries of many facets of the ubiquitous Brownian motion has revolutionized our fundamental understanding of the role of {\\it thermal fluctuations} in the exotic structures and complex dynamics exhibited by soft matter like, for example, colloids, gels, etc. The domain of B...
G- Brownian motion and Its Applications
EBRAHIMBEYGI, Atena; DASTRANJ, Elham
2015-01-01
Abstract. The concept of G-Brownian motion and G-Ito integral has been introduced by Peng. Also Ito isometry lemma is proved for Ito integral and Brownian motion. In this paper we first investigate the Ito isometry lemma for G-Brownian motion and G-Ito Integral. Then after studying of MG2,0-class functions [4], we introduce Stratonovich integral for G-Brownian motion,say G- Stratonovich integral. Then we present a special construction for G- Stratonovich integral.
Pricing European option under the time-changed mixed Brownian-fractional Brownian model
Guo, Zhidong; Yuan, Hongjun
2014-07-01
This paper deals with the problem of discrete time option pricing by a mixed Brownian-fractional subdiffusive Black-Scholes model. Under the assumption that the price of the underlying stock follows a time-changed mixed Brownian-fractional Brownian motion, we derive a pricing formula for the European call option in a discrete time setting.
Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations
Alkis, S.; Krause, J. L.; Fry, J. N.; Cheng, H.-P.
2009-03-01
We study the diffusion of silver nanoparticles on self-assembled monolayers (SAMs). Silver clusters Agn of sizes n=55 , 147, and 1289 were evolved in contact with an alkanethiol (12 carbon, dodecanethiol) SAM deposited on a gold (111) surface. Analysis based on classical molecular dynamics simulations reveals that these systems exhibit a rich variety of behaviors, from superdiffusive for the lightest cluster to pinned for the heaviest, evolution self-similar in lengths and times for the lightest cluster but with characteristic time scales and directional anisotropies emerging for the heavier clusters.
Traffic flow dynamics data, models and simulation
Treiber, Martin
2013-01-01
This textbook provides a comprehensive and instructive coverage of vehicular traffic flow dynamics and modeling. It makes this fascinating interdisciplinary topic, which to date was only documented in parts by specialized monographs, accessible to a broad readership. Numerous figures and problems with solutions help the reader to quickly understand and practice the presented concepts. This book is targeted at students of physics and traffic engineering and, more generally, also at students and professionals in computer science, mathematics, and interdisciplinary topics. It also offers material for project work in programming and simulation at college and university level. The main part, after presenting different categories of traffic data, is devoted to a mathematical description of the dynamics of traffic flow, covering macroscopic models which describe traffic in terms of density, as well as microscopic many-particle models in which each particle corresponds to a vehicle and its driver. Focus chapters on ...
Molecular dynamics simulations of weak detonations.
Am-Shallem, Morag; Zeiri, Yehuda; Zybin, Sergey V; Kosloff, Ronnie
2011-12-01
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal. PMID:22304055
Mobility Laws in Dislocation Dynamics Simulations
Energy Technology Data Exchange (ETDEWEB)
Cai, W; Bulatov, V V
2003-10-21
Prediction of the plastic deformation behavior of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, to establish a statistically representative model of crystal plasticity. A new massively-parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss an important ingredient of this code--the mobility laws dictating the behavior of individual dislocations. They are materials input for DD simulations and are constructed based on the understanding of dislocation motion at the atomistic level.
Mobility laws in dislocation dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Cai, Wei; Bulatov, Vasily V
2004-12-15
Prediction of the plastic deformation behavior of single crystals based on the collective dynamics of dislocations has been a challenge for computational materials science for a number of years. The difficulty lies in the inability of existing dislocation dynamics (DD) codes to handle a sufficiently large number of dislocation lines, to establish a statistically representative model of crystal plasticity. A new massively parallel DD code is developed that is capable of modeling million-dislocation systems by employing thousands of processors. We discuss an important ingredient of this code - the mobility laws dictating the behavior of individual dislocations. They are materials input for DD simulations and are constructed based on the understanding of dislocation motion at the atomistic level.
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
Molecular Dynamics Simulations for Predicting Surface Wetting
Directory of Open Access Journals (Sweden)
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Dynamic simulation of flywheel-type fuses
Directory of Open Access Journals (Sweden)
Editorial Office
1996-07-01
Full Text Available Rounds of ammunition are normally armed with a fuse. In this study, a fuse is developed which uses a flywheel-type mechanism controlled by time or distance. Due to its simplicity of operation and construction, the concept is expected to have high reliability. The dynamic response of all the components of this flywheel-type fuse is mathematically modelled. Simulation software was developed which connects the mathematical models of the various components. With the definition of boundary values, the response of the projectile, flywheel and other components can be determined continuously for firing and in-flight conditions.
Schwinger model simulations with dynamical overlap fermions
Energy Technology Data Exchange (ETDEWEB)
Bietenholz, W. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Shcheredin, S. [Bielefeld Univ. (Germany). Fakultaet fuer Physik; Volkholz, J. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik
2007-11-15
We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate {sigma} vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain - for the very light fermion masses - values for {sigma} that follow closely the analytical predictions in the continuum. (orig.)
Schwinger model simulations with dynamical overlap fermions
International Nuclear Information System (INIS)
We present simulation results for the 2-flavour Schwinger model with dynamical overlap fermions. In particular we apply the overlap hypercube operator at seven light fermion masses. In each case we collect sizable statistics in the topological sectors 0 and 1. Since the chiral condensate Σ vanishes in the chiral limit, we observe densities for the microscopic Dirac spectrum, which have not been addressed yet by Random Matrix Theory (RMT). Nevertheless, by confronting the averages of the lowest eigenvalues in different topological sectors with chiral RMT in unitary ensemble we obtain - for the very light fermion masses - values for Σ that follow closely the analytical predictions in the continuum. (orig.)
Dynamic Curving Simulation of Tilting Train
Zeng, Jing; Luo, Ren
The application of carbody tilting technology is the most efficient way to raise train speed during curve negotiations. This paper mainly deals with the dynamic performance simulation of the tilting train. Through the establishment of the nonlinear mathematical model for the titling train electromechanical coupled system, the carbody tilting control law, bogie radial steering mechanism, and titling train curving performance are investigated. The effect of time delay caused by the sensing and control system on the tilting performance of the train is analyzed, and the compensation methods for the time delay effect are studied.
Dynamic Deployment Simulations of Inflatable Space Structures
Wang, John T.
2005-01-01
The feasibility of using Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method in LSDYNA to simulate the dynamic deployment of inflatable space structures is investigated. The CV and ALE methods were used to predict the inflation deployments of three folded tube configurations. The CV method was found to be a simple and computationally efficient method that may be adequate for modeling slow inflation deployment sine the inertia of the inflation gas can be neglected. The ALE method was found to be very computationally intensive since it involves the solving of three conservative equations of fluid as well as dealing with complex fluid structure interactions.
Parallel Monte Carlo simulation of aerosol dynamics
Zhou, K.
2014-01-01
A highly efficient Monte Carlo (MC) algorithm is developed for the numerical simulation of aerosol dynamics, that is, nucleation, surface growth, and coagulation. Nucleation and surface growth are handled with deterministic means, while coagulation is simulated with a stochastic method (Marcus-Lushnikov stochastic process). Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI). The parallel computing efficiency is investigated through numerical examples. Near 60% parallel efficiency is achieved for the maximum testing case with 3.7 million MC particles running on 93 parallel computing nodes. The algorithm is verified through simulating various testing cases and comparing the simulation results with available analytical and/or other numerical solutions. Generally, it is found that only small number (hundreds or thousands) of MC particles is necessary to accurately predict the aerosol particle number density, volume fraction, and so forth, that is, low order moments of the Particle Size Distribution (PSD) function. Accurately predicting the high order moments of the PSD needs to dramatically increase the number of MC particles. 2014 Kun Zhou et al.
The probability of an encounter of two Brownian particles before escape
holcman, D
2009-01-01
We study the probability of two Brownian particles to meet before one of them exits a finite interval. We obtain an explicit expression for the probability as a function of the initial distance of the two particles using the Weierstrass elliptic function. We also find the law of the meeting location. Brownian simulations show the accuracy of our analysis. Finally, we discuss some applications to the probability that a double strand DNA break repairs in confined environments.
Non-Markovian weak coupling limit of quantum Brownian motion
Maniscalco, Sabrina; Piilo, Jyrki; Suominen, Kalle-Antti
2008-01-01
We derive and solve analytically the non-Markovian master equation for harmonic quantum Brownian motion proving that, for weak system-reservoir couplings and high temperatures, it can be recast in the form of the master equation for a harmonic oscillator interacting with a squeezed thermal bath. This equivalence guarantees preservation of positivity of the density operator during the time evolution and allows one to establish a connection between the dynamics of Schr\\"odinger cat states in sq...
Random Brownian scaling identities and splicing of Bessel processes
Pitman, Jim; Yor, Marc
1998-01-01
An identity in distribution due to Knight for Brownian motion is extended in two different ways: first by replacing the supremum of a reflecting Brownian motion by the range of an unreflected Brownian motion and second by replacing the reflecting Brownian motion by a recurrent Bessel process. Both extensions are explained in terms of random Brownian scaling transformations and Brownian excursions. The first extension is related to two different constructions of Itô’s law of ...
Nano-tribology through molecular dynamics simulations
Institute of Scientific and Technical Information of China (English)
WANG; Hui(
2001-01-01
［1］Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.［2］Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.［3］Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.［4］Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.［5］Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.［6］Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.［7］Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.［8］Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.［9］Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.［10］Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.［11］Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.［12］Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.［13］Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.
Dynamic simulation of tethered satellite systems
International Nuclear Information System (INIS)
The idea of connecting several spacecrafts by tethers to create mechanical systems with interesting dynamic properties was first brought up by Tsiolkovskii at the end of the nineteenth century, long before the technical means for realization were available. Today, after about 30 years of worldwide research, Tethered Satellite Systems have evolved into a promising technology with a considerable number of possible applications. These systems can be used to build large structures in orbit and provide a fuel-saving way of returning payloads from a space station. Conducting tethers interacting with the Earth's magnetic field can serve as motors or generators, transforming kinetic and electric energy into each other very efficiently. To develop this new technology seventeen experiments have been carried out in orbit since 1966 with NASA's TSS missions being the most well known. The work introduced in this thesis is part of a project carried out by the Institute of Mechanics of the Vienna University of Technology as contractor of the European Space Agency. A software package for the dynamic simulation of Tethered Satellite Systems with variable tether length has been developed to serve as a tool for the development and testing of such systems. The focus is on the deployment and retrieval of the tether, which is an important but tricky process, and has to be controlled by proper control algorithms. This can elegantly be done by a force acting on the tether at the point where it leaves the satellite. In the simulation program a mechanical model consisting of two satellites and a massive, perfectly flexible, visco-elastic tether is considered. The actual length of the tether is not given as a prescribed function of time but is an additional unknown and has to be calculated from the dynamics of the entire system and the forces acting on the tether. Hence the deployment mechanism has an important influence on the deployment dynamics. In this work the tether is considered to
Brownian colloids in underdamped and overdamped regimes with nonhomogeneous temperature
Sancho, J. M.
2015-12-01
The motion of Brownian particles when temperature is spatially dependent is studied by stochastic simulations and theoretical analysis. Nonequilibrium steady probability distributions Ps t(z ,v ) for both underdamped and overdamped regimes are analyzed. The existence of local kinetic energy equipartition theorem is also discussed. The transition between both regimes is characterized by a dimensionless friction parameter. This study is applied to three physical systems of colloidal particles.
Brownian motion of helical flagella.
Hoshikawa, H; Saito, N
1979-07-01
We develops a theory of the Brownian motion of a rigid helical object such as bacterial flagella. The statistical properties of the random forces acting on the helical object are discussed and the coefficients of the correlations of the random forces are determined. The averages , and are also calculated where z and theta are the position along and angle around the helix axis respectively. Although the theory is limited to short time interval, direct comparison with experiment is possible by using the recently developed cinematography technique. PMID:16997210
Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations.
Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong
2016-08-21
Herein we have used combined static electronic structure calculations and "on-the-fly" global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the (1)ππ(∗), (1)nπ(∗), and S0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated (1)ππ(∗) system. The first is the diabatic ESIPT process along the (1)ππ(∗) potential energy profile. The generated (1)ππ(∗) keto species then decays to the S0 state via the keto (1)ππ(∗)/gs conical intersection. The second is internal conversion to the dark (1)nπ(∗) state near the (1)ππ(∗) /(1)nπ(∗) crossing point in the course of the diabatic (1)ππ(∗) ESIPT process. Our following dynamics simulations have shown that the ESIPT and (1)ππ(∗) → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the (1)ππ(∗) → S0 internal conversion in the keto region, the (1)ππ(∗) → (1)nπ(∗) internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone. PMID:27544106
Quantum molecular dynamics simulations of dense matter
Energy Technology Data Exchange (ETDEWEB)
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Molecular Dynamic Simulation of Failure of Ettringite
International Nuclear Information System (INIS)
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
Molecular Dynamic Simulation of Failure of Ettringite
Sun, W.; Wang, D.; Wang, L.
2013-03-01
Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.
Reeves, Daniel B.; Weaver, John B.
2015-06-01
Magnetic nanoparticles are promising tools for a host of therapeutic and diagnostic medical applications. The dynamics of rotating magnetic nanoparticles in applied magnetic fields depend strongly on the type and strength of the field applied. There are two possible rotation mechanisms and the decision for the dominant mechanism is often made by comparing the equilibrium relaxation times. This is a problem when particles are driven with high-amplitude fields because they are not necessarily at equilibrium at all. Instead, it is more appropriate to consider the "characteristic timescales" that arise in various applied fields. Approximate forms for the characteristic time of Brownian particle rotations do exist and we show agreement between several analytical and phenomenological-fit models to simulated data from a stochastic Langevin equation approach. We also compare several approximate models with solutions of the Fokker-Planck equation to determine their range of validity for general fields and relaxation times. The effective field model is an excellent approximation, while the linear response solution is only useful for very low fields and frequencies for realistic Brownian particle rotations.
Intersection Exponents for Planar Brownian Motion
Lawler, Gregory F.; Werner, Wendelin
1999-01-01
We derive properties concerning all intersection exponents for planar Brownian motion and we define generalized exponents that, loosely speaking, correspond to noninteger numbers of Brownian paths. Some of these properties lead to general conjectures concerning the exact value of these exponents.
Dimensional Properties of Fractional Brownian Motion
Institute of Scientific and Technical Information of China (English)
Dong Sheng WU; Yi Min XIAO
2007-01-01
Let Bα = {Bα(t),t ∈ RN} be an (N,d)-fractional Brownian motion with Hurst index α∈ (0, 1). By applying the strong local nondeterminism of Bα, we prove certain forms of uniform Hausdorff dimension results for the images of Bα when N > αd. Our results extend those of Kaufman for one-dimensional Brownian motion.
Lessons Learned on Fuel Cycle Simulation Dynamics
Energy Technology Data Exchange (ETDEWEB)
Piet, S.J.; Dixon, B.W.; Jacobson, J.J.; Matthern, G.E.; Shropshire, D.E. [Idaho National Laboratory, 2525 North Fremont Mail Stop 3870, Idaho Falls, Idaho 83415-3870 (United States)
2009-06-15
Nuclear fuel cycles are inherently dynamic, yet many (if not most) comparisons of nuclear fuel cycle options compare them via static time-independent analyses. Instead, assessments need to consider dynamics in at least three senses - transitions from one fuel cycle strategy to another, how fuel cycles perform with nuclear power growth superimposed with time delays throughout the system, and variability of fuel cycle performance due to perturbations. This paper explains some of what we have learned from dynamic fuel cycle simulations using the VISION model. Dynamic analysis shows details not available through static analysis alone. - The fraction of fast reactors at any point in time will be much lower than predicted by simple 'static equilibrium' calculations due to multiple system constraints that impact the amount of TRU available for fueling new reactors at startup. - TRU management needs to account for both the TRU consumed in fast reactors and the additional TRU generation avoided due to fast reactors replacing some LWRs. - It is difficult to match the timing and size of deployment of reactors, separation plants, and fuel fabrication plants. - The holdup of transuranic material in the system impacts system performance so that short time lags (e.g. when facilities are co-located instead of at different locations) can lead to faster system evolution. - The higher the nuclear power growth rate, the higher the fast reactor TRU conversion ratio should be from the standpoint of uranium usage and the further the fast reactor fraction from static equilibrium. - The impact of transitioning to a closed fuel cycle on waste management is large and depends on processing loss rate and how long the closed fuel cycle has been implemented. - Fuel and separation facilities must accommodate variation in fuel mixture elemental composition. (authors)
On sequential dynamical systems and simulation
Energy Technology Data Exchange (ETDEWEB)
Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.
1999-06-01
The generic structure of computer simulations motivates a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper) which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes. This will be done using both combinatorial/algebraic techniques and probabilistic techniques. Finally the authors give results on dynamical system properties for some special systems.
Padding, J. T.; Louis, A. A.
2006-09-01
We describe in detail how to implement a coarse-grained hybrid molecular dynamics and stochastic rotation dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The importance of carefully tuning the simulation parameters to correctly resolve the multiple time and length scales of this problem is emphasized. We systematically analyze how our coarse-graining scheme resolves dimensionless hydrodynamic numbers such as the Reynolds number Re, which indicates the importance of inertial effects, the Schmidt number Sc, which indicates whether momentum transport is liquidlike or gaslike, the Mach number, which measures compressibility effects, the Knudsen number, which describes the importance of noncontinuum molecular effects, and the Peclet number, which describes the relative effects of convective and diffusive transport. With these dimensionless numbers in the correct regime the many Brownian and hydrodynamic time scales can be telescoped together to maximize computational efficiency while still correctly resolving the physically relevant processes. We also show how to control a number of numerical artifacts, such as finite-size effects and solvent-induced attractive depletion interactions. When all these considerations are properly taken into account, the measured colloidal velocity autocorrelation functions and related self-diffusion and friction coefficients compare quantitatively with theoretical calculations. By contrast, these calculations demonstrate that, notwithstanding its seductive simplicity, the basic Langevin equation does a remarkably poor job of capturing the decay rate of the velocity autocorrelation function in the colloidal regime, strongly underestimating it at short times and strongly overestimating it at long times. Finally, we discuss in detail how to map the parameters of our method onto physical systems and from this extract more general lessons—keeping in mind that there
Molecular dynamics simulations of shock compressed graphite
International Nuclear Information System (INIS)
We present molecular dynamic simulations of the shock compression of graphite with the LCBOPII potential. The range of shock intensities covers the full range of available experimental data, including near-tera-pascal pressures. The results are in excellent agreement with the available DFT data and point to a graphite-diamond transition for shock pressures above 65 GPa, a value larger than the experimental data (20 to 50 GPa). The transition mechanism leads preferentially to hexagonal diamond through a diffusion-less process but is submitted to irreversible re-graphitization upon release: this result is in good agreement with the lack of highly ordered diamond observed in post-mortem experimental samples. Melting is found for shock pressures ranging from 200 to 300 GPa, close to the approximate LCBOPII diamond melting line. A good overall agreement is found between the calculated and experimental Hugoniot data up to 46% compression rate. (authors)
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
Schwabe, Tobias
2015-08-20
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273
Simulation of reactor dynamic with temperature feedback
International Nuclear Information System (INIS)
In this simulations study, nonlinear system dynamics for pressurized Water Reactors was modeled by applying the finite element method to the two-group reactor dynamic equations in three-dimensions. The model is based on the Galerkin method in space-discretization and based on the temporal subdomain method in the discretization of time variable. Both Galerkin and temporal subdomain methods are special cases of more broad approach called weighted-residual methods. In the Galerkin's method, system space, and in the temporal subdomain method, time domain, are subdivided into subdomains called finite elements. Within each finite element of system space, unknown coefficient of space dependent shape functions are determined by making use of the shape functions of the neutron grup fluxes as weighting functions in residual integration. In the case of temporal subdomain method, unknown coefficients of time dependent shape functions are determined by making the residual orthogonal to the step functions. Spatial aspect of the problem was formulated in three-dimensional Cartesian coordinate system. Neutron fluxes are represented by bilinear polynomials in each rectangular prismatic finite element. In the study of feedback effects, due to the simulation of short transients, only contributions from fuel and coolant temperature changes were taken into account. The feedback contributions due to change in material cross-sections, effect of Xenon and similar changes are negligibly small to account for in such a short time interval. To include feedback mechanisms of fuel and coolant temperature variations, average fuel and coolant temperature variations, average fuel and coolant temperatures are calculated in each thermal-hydraulic region
Anomalous Brownian motion and viscoelasticity of the ear's mechanoelectrical transducer
Andor-Ardó, Daniel; Kozlov, Andrei; Hudspeth, A. J.
2009-03-01
The Brownian motion of a particle in a complex environment is known to display anomalous power-law scaling in which the mean squared displacement is proportional to a fractional power of time. Using laser interferometry and analytical methods of microrheology, we examine nanometer-scale thermal motions of hair bundles in the internal ear and show that these cellular organelles undergo fractional Brownian motion. This anomalous scaling is caused by viscoelasticity of the gating springs, elements that transmit energy in a sound to the mechanosensitive ion channels. These results demonstrate a connection between rheology and auditory physiology, and indicate that statistical properties of the thermal noise in the ear can be determined by dynamics of a small number of key molecules.
In silico FRET from simulated dye dynamics
Hoefling, Martin; Grubmüller, Helmut
2013-03-01
Single molecule fluorescence resonance energy transfer (smFRET) experiments probe molecular distances on the nanometer scale. In such experiments, distances are recorded from FRET transfer efficiencies via the Förster formula, E=1/(1+(). The energy transfer however also depends on the mutual orientation of the two dyes used as distance reporter. Since this information is typically inaccessible in FRET experiments, one has to rely on approximations, which reduce the accuracy of these distance measurements. A common approximation is an isotropic and uncorrelated dye orientation distribution. To assess the impact of such approximations, we present the algorithms and implementation of a computational toolkit for the simulation of smFRET on the basis of molecular dynamics (MD) trajectory ensembles. In this study, the dye orientation dynamics, which are used to determine dynamic FRET efficiencies, are extracted from MD simulations. In a subsequent step, photons and bursts are generated using a Monte Carlo algorithm. The application of the developed toolkit on a poly-proline system demonstrated good agreement between smFRET simulations and experimental results and therefore confirms our computational method. Furthermore, it enabled the identification of the structural basis of measured heterogeneity. The presented computational toolkit is written in Python, available as open-source, applicable to arbitrary systems and can easily be extended and adapted to further problems. Catalogue identifier: AENV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3, the bundled SIMD friendly Mersenne twister implementation [1] is provided under the SFMT-License. No. of lines in distributed program, including test data, etc.: 317880 No. of bytes in distributed program, including test data, etc.: 54774217 Distribution format: tar.gz Programming language
Simulation of relief valve dynamic behaviour
International Nuclear Information System (INIS)
Three heavy water spill incidents occurred at Wolsong-1, Pickering-A, and Bruce-A power plants in late 1994 and early 1995. In all incidents, the heavy water spills were caused by opening of the degasser/bleed condenser relief valves (RV). Detailed assessment of these incidents were carried out by the owners of the operating plants and by AECL. One of the key lessons learned from this assessments is that stable operation of the RVs is required to prevent damage to valve internals and associated piping resulting from water hammer/dynamic loads due to the RV chatter. The RV chatter phenomenon depends strongly on the performance characteristics of the valve, the associated piping configuration, and the operating conditions. To help understand and explain the chatter phenomenon, and to assist the evaluation of the dynamic behaviour of the existing or new RV installations, two RV models were developed and incorporated into the existing water hammer computer code, PTRAN. This paper describes the basic principle of the models and presents the simulation results in comparison with the test data. (author)
Human behavioral regularity, fractional Brownian motion, and exotic phase transition
Li, Xiaohui; Yang, Guang; An, Kenan; Huang, Jiping
2016-08-01
The mix of competition and cooperation (C&C) is ubiquitous in human society, which, however, remains poorly explored due to the lack of a fundamental method. Here, by developing a Janus game for treating C&C between two sides (suppliers and consumers), we show, for the first time, experimental and simulation evidences for human behavioral regularity. This property is proved to be characterized by fractional Brownian motion associated with an exotic transition between periodic and nonperiodic phases. Furthermore, the periodic phase echoes with business cycles, which are well-known in reality but still far from being well understood. Our results imply that the Janus game could be a fundamental method for studying C&C among humans in society, and it provides guidance for predicting human behavioral activity from the perspective of fractional Brownian motion.
Global dynamic load-balancing for decentralised distributed simulation
Bragard, Quentin; Ventresque, Anthony; Murphy, Liam
2014-01-01
Distributed simulations require partitioning mechanisms to operate, and the best partitioning algorithms try to load-balance the partitions. Dynamic load-balancing, i.e. re-partitioning simulation environments at run-time, becomes essential when the load in the partitions change. In decentralised distributed simulation the information needed to dynamically load-balance seems difficult to collect and to our knowledge, all solutions apply a local dynamic load balancing: partitions exchange load...
Overdamped limit and inverse-friction expansion for Brownian motion in an inhomogeneous medium.
Durang, Xavier; Kwon, Chulan; Park, Hyunggyu
2015-06-01
We revisit the problem of the overdamped (large-friction) limit of the Brownian dynamics in an inhomogeneous medium characterized by a position-dependent friction coefficient and a multiplicative noise (local temperature) in one-dimensional space. Starting from the Kramers equation and analyzing it through the expansion in terms of eigenfunctions of a quantum harmonic oscillator, we derive analytically the corresponding Fokker-Planck equation in the overdamped limit. The result is fully consistent with the previous finding by Sancho, San Miguel, and Dürr [J. Stat. Phys. 28, 291 (1982)]. Our method allows us to generalize the Brinkman's hierarchy, and thus it would be straightforward to obtain higher-order corrections in a systematic inverse-friction expansion without any assumption. Our results are confirmed by numerical simulations for simple examples. PMID:26172672
Computer Simulation of Fire Dynamics in Industrial Hall
International Nuclear Information System (INIS)
In this paper, computer simulation of smoke spread dynamics in industrial hall is investigated. A set of simulations of fire in three industrial halls with the same geometry varying in the height of ceiling is realized using the FDS fire simulator, version 6. The obtained simulation results are described focusing on the impact of the ceiling height and fire barriers on the fire course and smoke spread dynamics
Brownian motion meets Riemann curvature
International Nuclear Information System (INIS)
The general covariance of the diffusion equation is exploited in order to explore the curvature effects appearing in Brownian motion over a d-dimensional curved manifold. We use the local frame defined by the so-called Riemann normal coordinates to derive a general formula for the mean-square geodesic distance (MSD) at the short-time regime. This formula is written in terms of O(d) invariants that depend on the Riemann curvature tensor. We study the n-dimensional sphere case to validate these results. We also show that the diffusion for positive constant curvature is slower than the diffusion in a plane space, while the diffusion for negative constant curvature turns out to be faster. Finally the two-dimensional case is emphasized, as it is relevant for single-particle diffusion on biomembranes
New models and predictions for Brownian coagulation of non-interacting spheres.
Kelkar, Aniruddha V; Dong, Jiannan; Franses, Elias I; Corti, David S
2013-01-01
The classical steady-state Smoluchowski model for Brownian coagulation is evaluated using Brownian Dynamics Simulations (BDS) as a benchmark. The predictions of this approach compare favorably with the results of BDS only in the dilute limit, that is, for volume fractions of φ≤5×10(-4). From the solution of the more general unsteady-state diffusion equation, a new model for coagulation is developed. The resulting coagulation rate constant is time-dependent and approaches the steady-state limit only at large times. Moreover, in contrast to the Smoluchowski model, this rate constant depends on the particle size, with the transient effects becoming more significant at larger sizes. The predictions of the unsteady-state model agree well with the BDS results up to volume fractions of about φ=0.1, at which the aggregation half-time predicted by the Smoluchowski model is five times that of the BDS. A new procedure to extract the aggregation rate constant from simulation results based on this model is presented. The choice of the rate constant kernel used in the population balance equations for complete aggregation is also evaluated. Extension of the new model to a variable rate constant kernel leads to increased accuracy of the predictions, especially for φ≤5×10(-3). This size-dependence of the rate constant kernel affects particularly the predictions for initially polydisperse sphere systems. In addition, the model is extended to account in a novel way for both short-range viscous two-particle interactions and long-range many-particle Hydrodynamic Interactions (HI). Predictions including HI agree best with the BDS results. The new models presented here offer accurate and computationally less-intensive predictions of the coagulation dynamics while also accounting for hydrodynamic coupling. PMID:23036339
Simulation of reactor dynamics with temperature feedback
International Nuclear Information System (INIS)
-group three-dimensional reactor dynamics program that uses nodal method in the solution of reactor dynamics equations. Final aim of this work is to develop a general-purpose code with a controller and user interface for the analysis of a PWR core under normal or reactor trip conditions. Basically, the developed code simulates the two-group neutron dynamics equations coupled with six groups of delayed neutrons and temperature feedback in a three-dimensional Cartesian geometry by the use of the finite element method. Static eigenvalue computation part of the code is based on the work done by Oezgener's study [5]. In the approximation to the neutron flux bilinear polynomials are utilised and the space-dependent inner product operations are carried out by the Ritz method. In the space-time-dependent neutron dynamics formulation, however, discretization in space is based on the weighted-residual Galerkin method. In the discretization of the time domain the temporal sub domain method is utilised. The feedback effects are incorporated in such a way that the thermal-hydraulic channels and the thermal-hydraulic planes were defined with the use of finite elements where average fuel and average coolant temperatures will be calculated and included into the reactor dynamics equations. The developed program utilizes the finite element method fully in the space-time discretization of the reactor dynamics equations with temperature feedback. The symmetry property of half, quadrant or octant-core with any initial and/or boundary conditions can be used in the calculations. The thermal-hydraulic calculations are carried in separate axial hydraulic channels, each of which relates to one axial finite element. In the program, to represent a real reactor core by homogeneous regions with sufficient accuracy, fuel element number per each finite element, power generated in each finite element, number of thermal-hydraulic channels and mass flow rate per each thermal-hydraulic channel is calculated. In
Approaching the three-dimensional organization and dynamics of the human genome
T.A. Knoch (Tobias)
2008-01-01
textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fibre was folded according to the Mult
Approaching the Three-Dimensional Organization and Dynamics of the Human Genome
T.A. Knoch (Tobias)
2002-01-01
textabstractTo approach by virtual microscopy the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was fold
Approaching the Three-Dimensional Organization and Dynamics of the Human Genome
T.A. Knoch (Tobias)
2003-01-01
textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the M
Approaching the three-dimensional organization and dynamics of the human genome.
T.A. Knoch (Tobias)
2009-01-01
textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fibre was folded according to the Mul
Approaching the Three-Dimensional Organization and Dynamics of the Human Genome
T.A. Knoch (Tobias)
2002-01-01
textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the Mu
Approaching the Three-Dimensional Organization and Dynamics of the Human Genome
T.A. Knoch (Tobias)
2002-01-01
textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the M
Renewal Structure of the Brownian Taut String
Schertzer, Emmanuel
2015-01-01
In a recent paper, M. Lifshits and E. Setterqvist introduced the taut string of a Brownian motion $w$, defined as the function of minimal quadratic energy on $[0,T]$ staying in a tube of fixed width $h>0$ around $w$. The authors showed a Law of Large Number (L.L.N.) for the quadratic energy spent by the string for a large time $T$. In this note, we exhibit a natural renewal structure for the Brownian taut string, which is directly related to the time decomposition of the Brownian motion in te...
Nanoscale deicing by molecular dynamics simulation
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-07-01
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice
Simulation of burning plasma dynamics in ITER
International Nuclear Information System (INIS)
Dynamics of burning plasma for various transient situations in ITER plasma has been simulated with a 1.5-dimensional up-down asymmetry Tokamak Transport Simulation Code (TTSC). We have mainly paid attention to intrinsic plasma transport processes such as the confinement improvement and the change of plasma profiles. It is shown that a large excursion of the fusion power takes place with a small improvement of the plasma confinement; e.g., an increase of the global energy confinement by a factor of 1.22 yields the fusion power excursion of ∼ 30% within a few seconds. Any feedback control of fueling D-T gas is difficult to respond to this short time scale of fusion power transient. The effect of the plasma profile on the fusion power excursion has been studied, by changing the particle transport denoted by the inward pinch parameter CV. It is found that the fusion power excursion is mild and slow, and the feedback control is quite effective in suppressing the fusion power excursion and in shortening the duration time of power transient in this case. The change in the pumping efficiency has also been studied and a large excursion of the fusion power has not been observed, because of the decrease in the fuel density itself in the case of the increase in the pumping efficiency, and the helium ash accumulation in the case of the decrease in the pumping efficiency. Finally it is shown that the MHD sawteeth activity leads to the fusion power fluctuation of ± 20%, although it is helpful for the helium ash exhaust. (author)
Numerical simulation of magma chamber dynamics.
Longo, Antonella; Papale, Paolo; Montagna, Chiara Paola; Vassalli, Melissa; Giudice, Salvatore; Cassioli, Andrea
2010-05-01
Magma chambers are characterized by periodic arrivals of deep magma batches that give origin to complex patterns of magma convection and mixing, and modify the distribution of physical quantities inside the chamber. We simulate the transient, 2D, multi-component homogeneous dynamics in geometrically complex dyke+chamber systems, by means of GALES, a finite element parallel C++ code solving mass, momentum and energy equations for multi-component homogeneous gas-liquid (± crystals) mixtures in compressible-to-incompressible flow conditions. Code validation analysis includes several cases from the classical engineering literature, corresponding to a variety of subsonic to supersonic gas-liquid flow regimes (see http://www.pi.ingv.it/~longo/gales/gales.html). The model allows specification of the composition of the different magmas in the domain, in terms of ten major oxides plus the two volatile species H2O and CO2. Gas-liquid thermodynamics are modeled by using the compositional dependent, non-ideal model in Papale et al. (Chem.. Geol., 2006). Magma properties are defined in terms of local pressure, temperature, and composition including volatiles. Several applications are performed within domains characterized by the presence of one or more magma chambers and one or more dykes, with different geometries and characteristic size from hundreds of m to several km. In most simulations an initial compositional interface is placed at the top of a feeding dyke, or at larger depth, with the deeper magma having a lower density as a consequence of larger volatile content. The numerical results show complex patterns of magma refilling in the chamber, with alternating phases of magma ingression and magma sinking from the chamber into the feeding dyke. Intense mixing takes place in feeding dykes, so that the new magma entering the chamber is always a mixture of the deep and the initially resident magma. Buoyant plume rise occurs through the formation of complex convective
Dynamics Modeling of Heavy Special Driving Simulator
Institute of Scientific and Technical Information of China (English)
无
2008-01-01
Based on the dynamical characteristic parameters of the real vehicle, the modeling approach and procedure of dynamics of vehicles are expatiated. The layout of vehicle dynamics is proposed, and the sub-models of the diesel engine, drivetrain system and vehicle multi-body dynamics are introduced. Finally, the running characteristic data of the virtual and real vehicles are compared, which shows that the dynamics model is similar closely to the real vehicle system.
Annual Report 1999 Environmental Dynamics and Simulation
Energy Technology Data Exchange (ETDEWEB)
NS Foster-Mills
2000-06-28
This annual report describes selected 1999 research accomplishments for the Environmental Dynamics and Simulation (ED and S) directorate, one of six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). These accomplishments are representative of the different lines of research underway in the ED and S directorate. EMSL is one of US Department of Energy's (DOE) national scientific user facilities and is the centerpiece of DOE's commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems. Capabilities in the EMSL include over 100 major instrument systems for use by the resident research staff, their collaborators, and users of the EMSL. These capabilities are used to address the fundamental science that will be the basis for finding solutions to national environmental issues such as cleaning up contamianted areas at DOE sites across the country and developing green technologies that will reduce or eliminate future pollution production. The capabilities are also used to further the understanding of global climate change and environmental issues relevant to energy production and use and health effects resulting from exposure to contaminated environments.
Kinetic simulations of plasmoid chain dynamics
International Nuclear Information System (INIS)
The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids
Surface Structure of Hydroxyapatite from Simulated Annealing Molecular Dynamics Simulations.
Wu, Hong; Xu, Dingguo; Yang, Mingli; Zhang, Xingdong
2016-05-10
The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca(2+) ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules. PMID:27096760
Dynamic Simulation over Long Time Periods with 100% Solar Generation.
Energy Technology Data Exchange (ETDEWEB)
Concepcion, Ricky James [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Elliott, Ryan Thomas [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-12-01
This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.
Application of control theory to dynamic systems simulation
Auslander, D. M.; Spear, R. C.; Young, G. E.
1982-01-01
The application of control theory is applied to dynamic systems simulation. Theory and methodology applicable to controlled ecological life support systems are considered. Spatial effects on system stability, design of control systems with uncertain parameters, and an interactive computing language (PARASOL-II) designed for dynamic system simulation, report quality graphics, data acquisition, and simple real time control are discussed.
Experiences on dynamic simulation software in chemical engineering education
DEFF Research Database (Denmark)
Komulainen, Tiina M.; Enemark-rasmussen, Rasmus; Sin, Gürkan;
2012-01-01
Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics......: basic chemical engineering, operability and safety analysis and process control. User experiences from both teachers and students are presented. The benefits of dynamic simulation as an additional teaching tool are discussed and summarized. The experiences confirm that commercial dynamic simulators...... provide realistic training and can be successfully integrated into undergraduate and graduate teaching, laboratory courses and research....
Onsager coefficients of a Brownian Carnot cycle
Izumida, Yuki; Okuda, Koji
2010-01-01
We study a Brownian Carnot cycle introduced by T. Schmiedl and U. Seifert [Europhys. Lett. \\textbf{81}, 20003 (2008)] from a viewpoint of the linear irreversible thermodynamics. By considering the entropy production rate of this cycle, we can determine thermodynamic forces and fluxes of the cycle and calculate the Onsager coefficients for general protocols, that is, arbitrary schedules to change the potential confining the Brownian particle. We show that these Onsager coefficients contain the...
Some Finite Size Effects in Simulations of Glass Dynamics
Horbach, J.; Kob, W; Binder, K.; Angell, C.A.
1996-01-01
We present the results of a molecular dynamics computer simulation in which we investigate the dynamics of silica. By considering different system sizes, we show that in simulations of the dynamics of this strong glass former surprisingly large finite size effects are present. In particular we demonstrate that the relaxation times of the incoherent intermediate scattering function and the time dependence of the mean squared displacement are affected by such finite size effects. By compressing...
A real time autonomous underwater vehicle Dynamic Simulator
Jurewicz, Thomas A.
1990-01-01
The NPS Autonomous Underwater Vehicle Simulator is a joint project between the Naval Postgraduate School's Mechanical Engineering and Computer Science Departments. In order to test mission planning and execution software, an accurate vehicle dynamic model is required. Using dynamics based upon the Navy's Swimmer Delivery Vehicle (SDV), there is a need to continually update the hydrodynamic coefficients based upon actual vehicle-in-water testing. The NPS AUV Dynamic Simulator contains a full s...
Continuous Finite Element Methods of Molecular Dynamics Simulations
Qiong Tang; Luohua Liu; Yujun Zheng
2015-01-01
Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite elemen...
Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS
Astuti, A. D.; Mutiara, A. B.
2009-01-01
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example of molecular dynamics application developed by Groningen University. This application is a non-commercial and able to work in the operating system Linux. The main ability of Gromacs is to perform molecular dynamics simulation and minimization energy. In this...
Urbina-Villalba, German
2009-01-01
The first algorithm for Emulsion Stability Simulations (ESS) was presented at the V Conferencia Iberoamericana sobre Equilibrio de Fases y Diseño de Procesos [Luis, J.; García-Sucre, M.; Urbina-Villalba, G. Brownian Dynamics Simulation of Emulsion Stability In: Equifase 99. Libro de Actas, 1st Ed., Tojo J., Arce, A., Eds.; Solucion’s: Vigo, Spain, 1999; Volume 2, pp. 364–369]. The former version of the program consisted on a minor modification of the Brownian Dynamics algorithm to account for...
Simulation of chemical reaction dynamics on an NMR quantum computer
Lu, Dawei; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng
2011-01-01
Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.
Coulomb Friction Driving Brownian Motors
International Nuclear Information System (INIS)
We review a family of models recently introduced to describe Brownian motors under the influence of Coulomb friction, or more general non-linear friction laws. It is known that, if the heat bath is modeled as the usual Langevin equation (linear viscosity plus white noise), additional non-linear friction forces are not sufficient to break detailed balance, i.e. cannot produce a motor effect. We discuss two possibile mechanisms to elude this problem. A first possibility, exploited in several models inspired to recent experiments, is to replace the heat bath's white noise by a “collisional noise”, that is the effect of random collisions with an external equilibrium gas of particles. A second possibility is enlarging the phase space, e.g. by adding an external potential which couples velocity to position, as in a Klein—Kramers equation. In both cases, non-linear friction becomes sufficient to achieve a non-equilibrium steady state and, in the presence of an even small spatial asymmetry, a motor effect is produced. (general)
Brownian regime of finite-N corrections to particle motion in the XY hamiltonian mean field model
Ribeiro, Bruno V; Elskens, Yves
2016-01-01
We study the dynamics of the N-particle system evolving in the XY hamiltonian mean field (HMF) model for a repulsive potential, when no phase transition occurs. Starting from a homogeneous distribution, particles evolve in a mean field created by the interaction with all others. This interaction does not change the homogeneous state of the system, and particle motion is approximately ballistic with small corrections. For initial particle data approaching a waterbag, it is explicitly proved that corrections to the ballistic velocities are in the form of independent brownian noises over a time scale diverging not slower than $N^{2/5}$ as $N \\to \\infty$, which proves the propagation of molecular chaos. Molecular dynamics simulations of the XY-HMF model confirm our analytical findings.
Brownian regime of finite-N corrections to particle motion in the XY Hamiltonian mean field model
Ribeiro, Bruno V.; Amato, Marco A.; Elskens, Yves
2016-08-01
We study the dynamics of the N-particle system evolving in the XY Hamiltonian mean field (HMF) model for a repulsive potential, when no phase transition occurs. Starting from a homogeneous distribution, particles evolve in a mean field created by the interaction with all others. This interaction does not change the homogeneous state of the system, and particle motion is approximately ballistic with small corrections. For initial particle data approaching a waterbag, it is explicitly proved that corrections to the ballistic velocities are in the form of independent Brownian noises over a time scale diverging not slower than {N}2/5 as N\\to ∞ , which proves the propagation of molecular chaos. Molecular dynamics simulations of the XY-HMF model confirm our analytical findings.
Simulation analysis of a dynamic ridesharing model
Guasch Petit, Antonio; Figueras Jové, Jaume; Fonseca Casas, Pau; Montañola Sales, Cristina; Casanovas Garcia, Josep
2014-01-01
A dynamic ridesharing service is a system that enables drivers and riders to arrange one-time shared rides, with sufficient convenience and flexibility to be used on a daily basis. The quality of a dynamic ridesharing service is critical for commuters who need to reach their end destination on time every day. To ensure satisfactory quality, the waiting times in a ridesharing service must be low. This paper describes a dynamic ridesharing model proposal for commuters living in a small comm...
Continuous Finite Element Methods of Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Qiong Tang
2015-01-01
Full Text Available Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite element method is also a reliable method to simulate long-time classical trajectory of molecular systems.
Quasimolecular Dynamic Simulation for Bending Fracture of Laminar Composite Materials
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Recently, quasimolecular dynamics has been successfully used to simulate the deformation characteristics of actual size solid materials. In quasimolecular dynamics, which is an attempt to bridge the gap between atomistic and continuum simulations, molecules are aggregated into large units, called quasimolecules, to evaluate large scale material behavior. In this paper, a 2-dimensional numerical simulation using quasimolecular dynamics was performed to investigate laminar composite material fractures and crack propagation behavior in the uniform bending of laminar composite materials. It was verified that under bending deformation laminar composite materials deform quite differently from homogeneous materials
Salient Frame Detection for Molecular Dynamics Simulations
Kim, Youngmin; Patro, Robert; Yiu Ip, Cheuk; OLeary, Dianne P.; Anishkin, Andriy
2011-01-01
Recent advances in sophisticated computational techniques have facilitated simulation of incrediblydetailed time-varying trajectories and in the process have generated vast quantities of simulation data. The current tools to analyze and comprehend large-scale time-varying data, however, lag far behind our ability to produce such simulation data. Saliency-based analysis can be applied to time-varying 3D datasets for the purpose of summarization, abstraction, and motion analysis. As the sizes o...
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
International Nuclear Information System (INIS)
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed. (c) 1999 American Institute of Physics
Bewerunge, Jörg; Ladadwa, Imad; Platten, Florian; Zunke, Christoph; Heuer, Andreas; Egelhaaf, Stefan U
2016-07-28
Anomalous diffusion is a ubiquitous phenomenon in complex systems. It is often quantified using time- and ensemble-averages to improve statistics, although time averages represent a non-local measure in time and hence can be difficult to interpret. We present a detailed analysis of the influence of time- and ensemble-averages on dynamical quantities by investigating Brownian particles in a rough potential energy landscape (PEL). Initially, the particle ensemble is randomly distributed, but the occupancy of energy values evolves towards the equilibrium distribution. This relaxation manifests itself in the time evolution of time- and ensemble-averaged dynamical measures. We use Monte Carlo simulations to study particle dynamics in a potential with a Gaussian distribution of energy values, where the long-time limit of the diffusion coefficient is known from theory. In our experiments, individual colloidal particles are exposed to a laser speckle pattern inducing a non-Gaussian roughness and are followed by optical microscopy. The relaxation depends on the kind and degree of roughness of the PEL. It can be followed and quantified by the time- and ensemble-averaged mean squared displacement. Moreover, the heterogeneity of the dynamics is characterized using single-trajectory analysis. The results of this work are relevant for the correct interpretation of single-particle tracking experiments in general. PMID:27353405
Development Of Dynamic Probabilistic Safety Assessment: The Accident Dynamic Simulator (ADS) Tool
Energy Technology Data Exchange (ETDEWEB)
Chang, Y.H.; Mosleh, A.; Dang, V.N
2003-03-01
The development of a dynamic methodology for Probabilistic Safety Assessment (PSA) addresses the complex interactions between the behaviour of technical systems and personnel response in the evolution of accident scenarios. This paper introduces the discrete dynamic event tree, a framework for dynamic PSA, and its implementation in the Accident Dynamic Simulator (ADS) tool. Dynamic event tree tools generate and quantify accident scenarios through coupled simulation models of the plant physical processes, its automatic systems, the equipment reliability, and the human response. The current research on the framework, the ADS tool, and on Human Reliability Analysis issues within dynamic PSA, is discussed. (author)
Permutation entropy of fractional Brownian motion and fractional Gaussian noise
International Nuclear Information System (INIS)
We have worked out theoretical curves for the permutation entropy of the fractional Brownian motion and fractional Gaussian noise by using the Bandt and Shiha [C. Bandt, F. Shiha, J. Time Ser. Anal. 28 (2007) 646] theoretical predictions for their corresponding relative frequencies. Comparisons with numerical simulations show an excellent agreement. Furthermore, the entropy-gap in the transition between these processes, observed previously via numerical results, has been here theoretically validated. Also, we have analyzed the behaviour of the permutation entropy of the fractional Gaussian noise for different time delays
Additivity, density fluctuations, and nonequilibrium thermodynamics for active Brownian particles
Chakraborti, Subhadip; Mishra, Shradha; Pradhan, Punyabrata
2016-05-01
Using an additivity property, we study particle-number fluctuations in a system of interacting self-propelled particles, called active Brownian particles (ABPs), which consists of repulsive disks with random self-propulsion velocities. From a fluctuation-response relation, a direct consequence of additivity, we formulate a thermodynamic theory which captures the previously observed features of nonequilibrium phase transition in the ABPs from a homogeneous fluid phase to an inhomogeneous phase of coexisting gas and liquid. We substantiate the predictions of additivity by analytically calculating the subsystem particle-number distributions in the homogeneous fluid phase away from criticality where analytically obtained distributions are compatible with simulations in the ABPs.
Occupation times for planar and higher dimensional Brownian motion
International Nuclear Information System (INIS)
We consider a planar Brownian motion starting from O at time t = 0 and stopped at t. Denoting by T the time spent in a wedge of apex O and angle Θ, we develop a method to compute systematically the moments of T for general Θ values. We apply it to obtain analytically the second and third moments for a general wedge angle and, also, the fourth moment for the quadrant (Θ = π/2). We compare our results with numerical simulations. Finally, with standard perturbation theory, we establish a general formula for the second moment of an orthant occupation time
Moments of inertia and the shapes of Brownian paths
International Nuclear Information System (INIS)
The joint probability law of the principal moments of inertia of Brownian paths (open or closed) is computed, using constrained path integrals and Random Matrix Theory. The case of two-dimensional paths is discussed in detail. In particular, it is shown that the ratio of the average values of the largest and smallest moments is equal to 4.99 (open paths) and 3.07 (closed paths). Results of numerical simulations are also presented, which include investigation of the relationships between the moments of inertia and the arithmetic area enclosed by a path. (authors) 28 refs., 2 figs
Occupation times for planar and higher dimensional Brownian motion
Energy Technology Data Exchange (ETDEWEB)
Desbois, Jean [CNRS, University Paris Sud, UMR8626, LPTMS, ORSAY CEDEX, F-91405 (France)
2007-03-09
We consider a planar Brownian motion starting from O at time t = 0 and stopped at t. Denoting by T the time spent in a wedge of apex O and angle {theta}, we develop a method to compute systematically the moments of T for general {theta} values. We apply it to obtain analytically the second and third moments for a general wedge angle and, also, the fourth moment for the quadrant ({theta} = {pi}/2). We compare our results with numerical simulations. Finally, with standard perturbation theory, we establish a general formula for the second moment of an orthant occupation time.
Moments of inertia and the shapes of Brownian paths
Energy Technology Data Exchange (ETDEWEB)
Fougere, F.; Desbois, J.
1993-12-31
The joint probability law of the principal moments of inertia of Brownian paths (open or closed) is computed, using constrained path integrals and Random Matrix Theory. The case of two-dimensional paths is discussed in detail. In particular, it is shown that the ratio of the average values of the largest and smallest moments is equal to 4.99 (open paths) and 3.07 (closed paths). Results of numerical simulations are also presented, which include investigation of the relationships between the moments of inertia and the arithmetic area enclosed by a path. (authors) 28 refs., 2 figs.
Institute of Scientific and Technical Information of China (English)
熊海灵; 杨志敏; 李航
2015-01-01
耗时长是目前进行大规模体系分形凝聚模拟的主要障碍。该文采用优化存储结构来降低时间复杂度的思路，对传统On-lattice集团凝聚模型算法进行了改进。用三维数组表征模拟体系，用链表表征团簇结构，实现了在体系中直接访问任意团簇，以及确定组成团簇单粒在三维数组中对应数组元素具体位置的新方法。论文基于新的存储结构重新设计了集团凝聚模型中布朗运动、碰撞检测和凝聚的算法，使得模拟算法的总时间复杂度从立方阶变为了线性阶。该改进算法为研究人员进行大规模体系分形凝聚模拟提供了技术支撑。%The cluster-cluster aggregation (CCA) model bridges the study of colloid aggregation by computer simulation and laboratory experiment. Two distinct and limiting regimes of irreversible colloid aggregation have been identified by computer simulation with the CCA model. One regime is diffusion-limited cluster aggregation (DLCA) corresponding to the rapid colloid aggregation. The other is reaction-limited cluster aggregation (RLCA) corresponding to the slow colloid aggregation. The simulations of the two regimes are both start with N non-overlapping identical particles distributed randomly in a cubic box with side-lengths of L. A three dimensional array, hypothetically named Cube[L][L][L], was usually used to represent the cubic box. Each particle in the cubic box occupies an element of the three dimensional array and are labeled with a different integer. When particles and/or clusters collide and aggregate, all particles in the resulting cluster are modified with the same label (one of them). The progression of Brownian movement and aggregation are realized by updating the labels of the corresponding array elements. However, a critical issue in this kind of simulation is how to efficiently distinguish all of the particles in any selected cluster only based on the three dimensional array Cube
Mosquito population dynamics from cellular automata-based simulation
Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning
2016-02-01
In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.
Unified Nonlinear Flight Dynamics and Aeroelastic Simulator Tool Project
National Aeronautics and Space Administration — ZONA Technology, Inc. (ZONA) proposes a R&D effort to develop a Unified Nonlinear Flight Dynamics and Aeroelastic Simulator (UNFDAS) Tool that will combine...
Neutron Star Crust and Molecular Dynamics Simulation
Horowitz, C J; Schneider, A; Berry, D K
2011-01-01
In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.
Perspective: Computer simulations of long time dynamics
Energy Technology Data Exchange (ETDEWEB)
Elber, Ron [Department of Chemistry, The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712 (United States)
2016-02-14
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.
Perspective: Computer simulations of long time dynamics
International Nuclear Information System (INIS)
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances
Perspective: Computer simulations of long time dynamics.
Elber, Ron
2016-02-14
Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
Pabis, Anna; Geronimo, Inacrist; York, Darrin M.; Paneth, Piotr
2014-01-01
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specif...
ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.
Directory of Open Access Journals (Sweden)
Johannes Schöneberg
Full Text Available We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.
Visual Dynamic Simulation and Optimization of Zhangjiuhe Diversion Project
Institute of Scientific and Technical Information of China (English)
ZHONG Denghua; LIU Jianmin; XIONG Kaizhi; FU Jinqiang
2008-01-01
With the aim of visualizing the real-time simulation calculation of water delivery system (WDS), a structural drawing-oriented (SDO) simulation technique was presented, and applied to Zhangjiuhe Diversion Project, which is a long-distance water delivery system constructed for drawing water from the Zhangjiuhe River to Kunming city. Taking SIMULINK software as simulating platform, the technique established a visual dynamic simulation model for the system. The simulation procedure of the system was simplified, and the efficiency of modeling was also enhanced according to the modularization and reutilization of the simulation program. Furthermore, a selfoptimization model was presented. Based on the digital simulation models, the on line controlled optimization link was added, and the input data can be continually optimized according to the feedback information of simulating output. The system was thus optimized automatically. Built upon MATLAB software, simulation optimization of the Zhangjiuhe Diversion Project was achieved, which provides a new way for the research of optimal operation of WDS.
3D Molecular dynamics simulations using spheropolytopes
Galindo-Torres, Sergio-Andres; Alonso-Marroquin, Fernando; Wang, Yucang
2008-01-01
We present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple concepts of computational geometry. The model (particles + interactions) is efficient, accurate and easy to implement, and it complies with the conservation laws of physics. 3D simulations of hopper flow shows that the non-convexity of the particles strong...
Dynamic fault simulation of wind turbines using commercial simulation tools
DEFF Research Database (Denmark)
Lund, Torsten; Eek, Jarle; Uski, Sanna;
2005-01-01
This paper compares the commercial simulation tools: PSCAD/EMTDC, PowerFactory, SIMPOW and PSS/E for analysing fault sequences defined in the Danish grid code requirements for wind turbines connected to a voltage level below 100 kV. Both symmetrical and unsymmetrical faults are analysed. The devi...
Stochastic optimal control problem with infinite horizon driven by G-Brownian motion
Hu, Mingshang; Wang, Falei
2016-01-01
The present paper considers a stochastic optimal control problem, in which the cost function is defined through a backward stochastic differential equation with infinite horizon driven by G-Brownian motion. Then we study the regularities of the value function and establish the dynamic programming principle. Moreover, we prove that the value function is the uniqueness viscosity solution of the related HJBI equation.
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
Energy Technology Data Exchange (ETDEWEB)
Lau, E Y; Krishnan, V V
2007-07-18
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
Holographic Brownian Motion in Three-Dimensional Gödel Black Hole
International Nuclear Information System (INIS)
By using the AdS/CFT correspondence and Gödel black hole background, we study the dynamics of heavy quark under a rotating plasma. In that case we follow Atmaja (2013) about Brownian motion in BTZ black hole. In this paper we receive some new results for the case of α2l2≠1. In this case, we must redefine the angular velocity of string fluctuation. We obtain the time evolution of displacement square and angular velocity and show that it behaves as a Brownian particle in non relativistic limit. In this plasma, it seems that relating the Brownian motion to physical observables is rather a difficult work. But our results match with Atmaja work in the limit α2l2→1
Collective dynamics effect transient subdiffusion of inert tracers in flexible gel networks
Godec, Aljaž; Bauer, Maximilian; Metzler, Ralf
2014-09-01
Based on extensive Brownian dynamics simulations we study the thermal motion of a tracer bead in a cross-linked, flexible gel in the limit when the tracer particle size is comparable to or even larger than the equilibrium mesh size of the gel. The analysis of long individual trajectories of the tracer demonstrates the existence of pronounced transient anomalous diffusion. From the time averaged mean squared displacement and the time averaged van Hove correlation functions we elucidate the many-body origin of the non-Brownian tracer bead dynamics. Our results shed new light onto the ongoing debate over the physical origin of steric tracer interactions with structured environments.
Energy conservation in molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren; Heilmann, Ole; Dyre, J. C.
2012-01-01
Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...
Stability of excited nuclei in a dynamical simulation
International Nuclear Information System (INIS)
We investigate the stability of excited 197Au nuclei with respect to multifragmentation using a dynamical simulation based on molecular dynamics and restructured aggregation. We focus attention on 3 kinds of excitations: heat, compression and rotation. We also study the influence of a geometrical perturbation created when a projectile drills a hole in a 197Au nucleus
Engineering Autonomous Chemomechanical Nanomachines Using Brownian Ratchets
Lavella, Gabriel
Nanoscale machines which directly convert chemical energy into mechanical work are ubiquitous in nature and are employed to perform a diverse set of tasks such as transporting molecules, maintaining molecular gradients, and providing motion to organisms. Their widespread use in nature suggests that large technological rewards can be obtained by designing synthetic machines that use similar mechanisms. This thesis addresses the technological adaptation of a specific mechanism known as the Brownian ratchet for the design of synthetic autonomous nanomachines. My efforts were focused more specifically on synthetic chemomechanical ratchets which I deem will be broadly applicable in the life sciences. In my work I have theoretically explored the biophysical mechanisms and energy landscapes that give rise to the ratcheting phenomena and devised devices that operate off these principles. I demonstrate two generations of devices that produce mechanical force/deformation in response to a user specified ligand. The first generation devices, fabricatied using a combination nanoscale lithographic processes and bioconjugation techniques, were used to provide evidence that the proposed ratcheting phenomena can be exploited in synthetic architectures. Second generation devices fabricated using self-assembled DNA/hapten motifs were constructed to gain a precise understanding of ratcheting dynamics and design constraints. In addition, the self-assembled devices enabled fabrication en masse, which I feel will alleviate future experimental hurdles in analysis and facilitate its adaptation to technologies. The product of these efforts is an architecture that has the potential to enable numerous technologies in biosensing and drug delivery. For example, the coupling of molecule-specific actuation to the release of drugs or signaling molecules from nanocapsules or porous materials could be transformative. Such architectures could provide possible avenues to pressing issues in biology and
Simulation of dynamics of hydraulic system with proportional control valve
Bureček Adam; Hružík Lumír; Vašina Martin
2016-01-01
Dynamics of a hydraulic system is influenced by several parameters, in this case mainly by proportional control valve, oil bulk modulus, oil viscosity, mass load etc. This paper will be focused on experimental measurement and mathematical simulation of dynamics of a hydraulic system with proportional control valve, linear hydraulic cylinder and mass load. The measurement is performed on experimental equipment that enables realization of dynamic processes of the hydraulic system. Linear hydrau...
N-body simulations in modified Newtonian dynamics
Nipoti, Carlo; Londrillo, Pasquale; Ciotti, Luca
2008-01-01
We describe some results obtained with N-MODY, a code for N-body simulations of collisionless stellar systems in modified Newtonian dynamics (MOND). We found that a few fundamental dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter. In particular, violent relaxation, phase mixing and galaxy merging take significantly longer in MOND than in Newtonian gravity, while dynamical friction is more effective in a MOND system than in an equivalent Newtonian ...
N-body simulations in modified Newtonian dynamics
Nipoti, Carlo; Ciotti, Luca
2008-01-01
We describe some results obtained with N-MODY, a code for N-body simulations of collisionless stellar systems in modified Newtonian dynamics (MOND). We found that a few fundamental dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter. In particular, violent relaxation, phase mixing and galaxy merging take significantly longer in MOND than in Newtonian gravity, while dynamical friction is more effective in a MOND system than in an equivalent Newtonian system with dark matter.
A Process for Comparing Dynamics of Distributed Space Systems Simulations
Cures, Edwin Z.; Jackson, Albert A.; Morris, Jeffery C.
2009-01-01
The paper describes a process that was developed for comparing the primary orbital dynamics behavior between space systems distributed simulations. This process is used to characterize and understand the fundamental fidelities and compatibilities of the modeling of orbital dynamics between spacecraft simulations. This is required for high-latency distributed simulations such as NASA s Integrated Mission Simulation and must be understood when reporting results from simulation executions. This paper presents 10 principal comparison tests along with their rationale and examples of the results. The Integrated Mission Simulation (IMSim) (formerly know as the Distributed Space Exploration Simulation (DSES)) is a NASA research and development project focusing on the technologies and processes that are related to the collaborative simulation of complex space systems involved in the exploration of our solar system. Currently, the NASA centers that are actively participating in the IMSim project are the Ames Research Center, the Jet Propulsion Laboratory (JPL), the Johnson Space Center (JSC), the Kennedy Space Center, the Langley Research Center and the Marshall Space Flight Center. In concept, each center participating in IMSim has its own set of simulation models and environment(s). These simulation tools are used to build the various simulation products that are used for scientific investigation, engineering analysis, system design, training, planning, operations and more. Working individually, these production simulations provide important data to various NASA projects.
Dynamics of a compound vesicle: numerical simulations
Veerapaneni, Shravan; Young, Yuan-Nan; Vlahovska, Petia; Blawzdziewicz, Jerzy
2010-11-01
Vesicles (self-enclosing lipid membranes) in simple linear flows are known to exhibit rich dynamics such as tank-treading, tumbling, trembling (swinging), and vacillating breathing. Recently, vesicles have been used as a multi-functional platform for drug-delivery. In this work, the dynamics of simplified models for such compound vesicles is investigated numerically using a state-of-the-art boundary-integral code that has been validated with high accuracy and efficiency. Results show that for a vesicle enclosing a rigid particle in a simple shear flow, transition from tank-treading to tumbling is possible even in the absence of viscosity mismatch in the interior and exterior fluids. We will discuss the shape transformations, multiple particle interactions and the flow properties. Comparison with results from analytical modeling gives insights to the underlying physics for such novel dynamics.
International Nuclear Information System (INIS)
The moment method can be used to determine the time evolution of particle size distribution due to Brownian coagulation based on the general dynamic equation (GDE). But the function form of the initial particle size distribution must be determined beforehand for the moment method. If the assumed function type of the initial particle size distribution has an obvious deviation from the true particle population, the evolution of particle size distribution may be different from the real evolution tendency. Thus, a simple and general method is proposed based on the moment method. In this method, the Johnson's SB function is chosen as a general distribution function to fit the initial distributions including the log normal (L-N), Rosin–Rammler (R-R), normal (N-N) and gamma distribution functions, respectively. Meanwhile, using the modified beta function to fit the L-N, R-R, N-N and gamma functions is also conducted as a comparison in order to present the advantage of the Johnson's SB function as the general distribution function. And then, the time evolution of particle size distributions using the Johnson's SB function as the initial distribution can be obtained by several lower order moment equations of the Johnson's SB function in conjunction with the GDE during the Brownian coagulation process. Simulation experiments indicate that fairly reasonable results of the time evolution of particle size distribution can be obtained with this proposed method in the free molecule regime, transition regime and continuum plus near continuum regime, respectively, at the early time stage of evolution. The Johnson's SB function has the ability of describing the early time evolution of different initial particle size distributions. (paper)
Active site modeling in copper azurin molecular dynamics simulations
Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R
2004-01-01
Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po
Dynamical simulations with HYP-link Wilson fermions
International Nuclear Information System (INIS)
We present results from simulations of two dynamical flavors of improvedWilson fermions with nHYP smeared gauge links. We demonstrate that the simulation is stable at a pseudo-scalar mass of 360 MeV, a 2.1 fm box and a lattice spacing of 0.13 fm. (orig.)
Dynamic wind turbine models in power system simulation tool
DEFF Research Database (Denmark)
Hansen, A.; Jauch, Clemens; Soerensen, P.; Iov, Florin; Blaabjerg, Frede
The present report describes the dynamic wind turbine models implemented in the power system simulation tool DIgSILENT. The developed models are a part of the results of a national research project, whose overall objective is to create a model database in different simulation tools. The report...
Brownian semistationary processes and volatility/intermittency
DEFF Research Database (Denmark)
Barndorff-Nielsen, Ole Eiler; Schmiegel, Jürgen
A new class of stochastic processes, termed Brownian semistationary processes (BSS), is introduced and discussed. This class has similarities to that of Brownian semimartingales (BSM), but is mainly directed towards the study of stationary processes, and BSS processes are not in general of the...... turbulent velocity fields and is the purely temporal version of the general tempo-spatial framework of ambit processes. The latter, which may have applications also to the finance of energy markets, is briefly considered at the end of the paper, again with reference to the question of inference on the...
Diffusion of torqued active Brownian particles
Sevilla, Francisco J.
An analytical approach is used to study the diffusion of active Brownian particles that move at constant speed in three-dimensional space, under the influence of passive (external) and active (internal) torques. The Smoluchowski equation for the position distribution of the particles is obtained from the Kramer-Fokker-Planck equation corresponding to Langevin equations for active Brownian particles subject to torques. In addition of giving explicit formulas for the mean square-displacement, the non-Gaussian behavior is analyzed through the kurtosis of the position distribution that exhibits an oscillatory behavior in the short-time limit. FJS acknowledges support from PAPIIT-UNAM through the grant IN113114
Aurell, E; Noullez, A; Blank, M
1996-01-01
It is shown that the inverse Lagrangian map for the solution of the Burgers equation (in the inviscid limit) with Brownian initial velocity presents a bifractality (phase transition) similar to that of the Devil's staircase for the standard triadic Cantor set. Both heuristic and rigorous derivations are given. It is explained why artifacts can easily mask this phenomenon in numerical simulations.
Bertrand, Pierre R; Guillin, Arnaud
2010-01-01
We investigate here the Central Limit Theorem of the Increment Ratio Statistic of a multifractional Brownian motion, leading to a CLT for the time varying Hurst index. The proofs are quite simple relying on Breuer-Major theorems and an original freezing of time strategy. A simulation study shows the goodness of fit of this estimator.
Semiconductor nanostructure properties. Molecular Dynamic Simulations
International Nuclear Information System (INIS)
The need for research is based on the fact that development of non-planar semiconductor nanosystems and nanomaterials with controlled properties is an important scientific and industrial problem. So, final scientific and technological problem is the creation of adequate modern methods and software for growth and properties simulation and optimization of various III-V (GaAs, InAs, InP, InGaAs etc.) nanostructures (e.g. nanowires) with controlled surface morphology, crystal structure, optical, transport properties etc. Accordingly, now we are developing a specialized computer code for atomistic simulation of structural (distribution of atoms and impurities, elastic and force constants, strain distribution etc.) and thermodynamic (mixing energy, interaction energy, surface energy etc.) properties of the nanostructures. Some simulation results are shown too
Intermittency and multifractional Brownian character of geomagnetic time series
Directory of Open Access Journals (Sweden)
G. Consolini
2013-07-01
Full Text Available The Earth's magnetosphere exhibits a complex behavior in response to the solar wind conditions. This behavior, which is described in terms of mutifractional Brownian motions, could be the consequence of the occurrence of dynamical phase transitions. On the other hand, it has been shown that the dynamics of the geomagnetic signals is also characterized by intermittency at the smallest temporal scales. Here, we focus on the existence of a possible relationship in the geomagnetic time series between the multifractional Brownian motion character and the occurrence of intermittency. In detail, we investigate the multifractional nature of two long time series of the horizontal intensity of the Earth's magnetic field as measured at L'Aquila Geomagnetic Observatory during two years (2001 and 2008, which correspond to different conditions of solar activity. We propose a possible double origin of the intermittent character of the small-scale magnetic field fluctuations, which is related to both the multifractional nature of the geomagnetic field and the intermittent character of the disturbance level. Our results suggest a more complex nature of the geomagnetic response to solar wind changes than previously thought.
Flexing Computational Muscle: Modeling and Simulation of Musculotendon Dynamics
Millard, Matthew; Uchida, Thomas; Seth, Ajay; Delp, Scott L.
2013-01-01
Muscle-driven simulations of human and animal motion are widely used to complement physical experiments for studying movement dynamics. Musculotendon models are an essential component of muscle-driven simulations, yet neither the computational speed nor the biological accuracy of the simulated forces has been adequately evaluated. Here we compare the speed and accuracy of three musculotendon models: two with an elastic tendon (an equilibrium model and a damped equilibrium model) and one with ...
Simulation of chemical reaction dynamics on an NMR quantum computer
Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng
2011-01-01
Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical ...
Molecular dynamics simulation study of polyelectrolyte adsorption on cellulose surfaces
Biermann, Oliver
2002-01-01
The adsorption of two polyelectrolyte ((carboxy methyl) cellulose and poly(acrylate) in water on crystalline cellulose is studied in this work. The multi-component problem has been splitted up into simulations of solutions of the polyelectrolyte (polyanions including sodium counterions) in water, into simulations of the interface of crystalline cellulose towards water. Finally polyelectrolyte-cellulose systems were studied. Molecular dynamics simulations of diluted (_ 2:5 weight percent) aque...
An attempt toward the generalized Langevin dynamics simulation
Directory of Open Access Journals (Sweden)
B.Kim
2008-03-01
Full Text Available An attempt to generalize the Langevin dynamics simulation method is presented based on the generalized Langevin theory of liquids, in which the dynamics of both solute and solvent is treated by the generalized Langevin equations, but the integration of the equation of motion of solute is made in the manner similar to the ordinary molecular dynamics simulation with discretized time steps along a trajectory. A preliminary result is derived based on an assumption of the uniform solvent density. The result is regarded to be a microscopic generalization of the phenomenological Langevin theory for the harmonic oscillator immersed in a continuum solvent developed by Wang and Uhlenbeck.
Topology in dynamical lattice QCD simulations
Energy Technology Data Exchange (ETDEWEB)
Gruber, Florian
2012-08-20
Lattice simulations of Quantum Chromodynamics (QCD), the quantum field theory which describes the interaction between quarks and gluons, have reached a point were contact to experimental data can be made. The underlying mechanisms, like chiral symmetry breaking or the confinement of quarks, are however still not understood. This thesis focuses on topological structures in the QCD vacuum. Those are not only mathematically interesting but also closely related to chiral symmetry and confinement. We consider methods to identify these objects in lattice QCD simulations. Based on this, we explore the structures resulting from different discretizations and investigate the effect of a very strong electromagnetic field on the QCD vacuum.
Kinetic Monte Carlo simulation of dislocation dynamics
International Nuclear Information System (INIS)
A kinetic Monte Carlo simulation of dislocation motion is introduced. The dislocations are assumed to be composed of pure edge and screw segments confined to a fixed lattice. The stress and temperature dependence of the dislocation velocity is studied, and finite-size effects are discussed. It is argued that surfaces and boundaries may play a significant role in the velocity of dislocations. The simulated dislocations are shown to display kinetic roughening according to the exponents predicted by the Kardar-Parisi-Zhang equation. copyright 1999 The American Physical Society
Topology in dynamical lattice QCD simulations
International Nuclear Information System (INIS)
Lattice simulations of Quantum Chromodynamics (QCD), the quantum field theory which describes the interaction between quarks and gluons, have reached a point were contact to experimental data can be made. The underlying mechanisms, like chiral symmetry breaking or the confinement of quarks, are however still not understood. This thesis focuses on topological structures in the QCD vacuum. Those are not only mathematically interesting but also closely related to chiral symmetry and confinement. We consider methods to identify these objects in lattice QCD simulations. Based on this, we explore the structures resulting from different discretizations and investigate the effect of a very strong electromagnetic field on the QCD vacuum.
Generalized Einstein Relation for Brownian Motion in Tilted Periodic Potential
Sakaguchi, Hidetsugu
2006-01-01
A generalized Einstein relation is studied for Brownian motion in a tilted potential. The exact form of the diffusion constant of the Brownian motion is compared with the generalized Einstein relation. The generalized Einstein relation is a good approximation in a parameter range where the Brownian motion exhibits stepwise motion.
Kolmogorov complexity and the geometry of Brownian motion
Fouche, Willem L.
2014-01-01
In this paper, we continue the study of the geometry of Brownian motions which are encoded by Kolmogorov-Chaitin random reals (complex oscillations). We unfold Kolmogorov-Chaitin complexity in the context of Brownian motion and specifically to phenomena emerging from the random geometric patterns generated by a Brownian motion.
Magnetization direction in the Heisenberg model exhibiting fractional Brownian motion
DEFF Research Database (Denmark)
Zhang, Zhengping; Mouritsen, Ole G.; Zuckermann, Martin J.
1993-01-01
ferromagnetic phase characterizing fractional Brownian motion, whereas a value H congruent-to 0. 5, reflecting ordinary Brownian motion, applies in the paramagnetic phase. A field-induced crossover from fractional to ordinary Brownian motion has been observed in the ferromagnetic phase....
Simulation analysis of dynamic working performance for star trackers.
Shen, Juan; Zhang, Guangjun; Wei, Xinguo
2010-12-01
The elongated imaging track pertaining to a star spot recorded in the image sensor of a star tracker will diffuse over several pixels at a high angular velocity, leading to an inaccurate, even false, attitude value. A computer simulation of the attitude determination from a dynamic star tracker is developed first, based on a dynamic mathematical model of the star-spot imaging and an efficiency validation of the star centroiding algorithm in the dynamic condition. Then major error sources affecting the attitude accuracy in the dynamic condition are analyzed and discussed systematically based on the simulation results. A mathematical model calculating the average star number detected in the field of view is also deduced, using simulation results and signal processing theory, with image trailing ranging from 0 to 20 pixels during exposure. The summarized regularity is helpful in the system design and accuracy evaluation of a star tracker. PMID:21119749
Dynamic simulation of steam generator failures
International Nuclear Information System (INIS)
A computer program will be described which is capable to simulate severe transients in a gas heated steam generator. Such transients may arise in the safety analysis of accidents resulting from failures in the heat removal system of an HTGR power plant. Important failure modes which have to be considered are ruptures of one or more steam generator tubes leading to water or steam ejection into the primary system or anomalous operating conditions which my cause damage due to excessive thermal stress. Examples are the complete dryout as a consequence of feedwater interrupt in connection with continuing gas heating and the reflooding of the secondary channel with cold feedwater after dryout. The steam generator program which is capable to simulate accidents of this type is written as a module which can be implemented into a program system fur the simulation of the total heat rejection system. It based on an advanced mathematical model for the two phase flow taking deviations from thermal equilibrium into account. Mass, energy and momentum balances for the primary and secondary fluid and the heat diffusion equations for the heat exchanging wall form a system of coupled differential equations which is solved numerically by an algorithm which is stiffly stable and suppresses effectively oscillations of numerical origin. Results of the simulation of transients of the type mentioned above will be presented and discussed. (author)
New ways to boost molecular dynamics simulations
Krieger, E.; Vriend, G.
2015-01-01
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 A cutoff, correct
Simulations of dislocation dynamics in aluminum interconnects
Nicola, L; Van der Giessen, E; Needleman, A; Zavaliangos, A; Tikare,; Olevsky, EA
2002-01-01
A discrete dislocation simulation of plastic deformation in metallic interconnects caused by thermal stress is carried out. The calculations are carried out using a two dimensional plane strain formulation with only edge dislocations. A boundary value problem is formulated and solved for the evoluti
Programmable quantum simulation by dynamic Hamiltonian engineering
Hayes, David; Flammia, Steven T.; Biercuk, Michael J.
2014-08-01
Quantum simulation is a promising near term application for quantum information processors with the potential to solve computationally intractable problems using just a few dozen interacting qubits. A range of experimental platforms have recently demonstrated the basic functionality of quantum simulation applied to quantum magnetism, quantum phase transitions and relativistic quantum mechanics. However, in all cases, the physics of the underlying hardware restricts the achievable inter-particle interactions and forms a serious constraint on the versatility of the simulators. To broaden the scope of these analog devices, we develop a suite of pulse sequences that permit a user to efficiently realize average Hamiltonians that are beyond the native interactions of the system. Specifically, this approach permits the generation of all symmetrically coupled translation-invariant two-body Hamiltonians with homogeneous on-site terms, a class which includes all spin-1/2 XYZ chains, but generalized to include long-range couplings. Our work builds on previous work proving that universal simulation is possible using both entangling gates and single-qubit unitaries. We show that determining the appropriate ‘program’ of unitary pulse sequences which implements an arbitrary Hamiltonian transformation can be formulated as a linear program over functions defined by those pulse sequences, running in polynomial time and scaling efficiently in hardware resources. Our analysis extends from circuit model quantum information to adiabatic quantum evolutions, representing an important and broad-based success in applying functional analysis to the field of quantum information.
Molecular Dynamics Simulation of Amyloid Beta Dimer Formation
Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V
2004-01-01
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Institute of Scientific and Technical Information of China (English)
张莉莉; 张建华; 周林祥
2002-01-01
We have carried out parallel molecular dynamics simulations of solvated and non-solvated myoglobin and solvated Cu/Zn superoxide dismutase at different temperatures. By analysis of several methods, the simulations reproduce the quasielastic neutron scattering experimental results. Below 200 K these two proteins behave as harmonic solids with essentially only vibrational motion, while above this temperature, there is a striking dynamic transition into anharmonic motion. Moreover, the simulations further show that water molecules play an important role for this dynamical transition. There is no such sharp dynamical transition in non-solvated proteins and the higher the solvate density is, the steeper at transition point the curve of mean square displacement versus temperature will be. The simulations also display that the dynamical transition is a general property for globular protein and this transition temperature is a demarcation of enzyme activity.
Stadler, A.M.; Garvey, C J; Bocahut, A.; Sacquin-Mora, S.; Digel, I.; Schneider, G. J.; Natali, F.; Artmann, G. M.; Zaccai, G.
2012-01-01
Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus; domestic chicken, Gallus gallus domesticus and human, Homo sapiens) and an ectotherm (salt water crocodile, Crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein re...
Altintas, Ersin; Böhringer, Karl F.; Fujita, Hiroyuki
2008-11-01
Nanosystems operating in liquid media may suffer from random Brownian motion due to thermal fluctuations. Biomolecular motors exploit these random fluctuations to generate a controllable directed movement. Inspired by nature, we proposed and realized a nano-system based on Brownian motion of nanobeads for linear transport in microfluidic channels. The channels limit the degree-of-freedom of the random motion of beads into one dimension, which was rectified by a three-phase dielectrophoretic ratchet biasing the spatial probability distribution of the nanobead towards the transportation direction. We micromachined the proposed device and experimentally traced the rectified motion of nanobeads and observed the shift in the bead distribution as a function of applied voltage. We identified three regions of operation; (1) a random motion region, (2) a Brownian motor region, and (3) a pure electric actuation region. Transportation in the Brownian motor region required less applied voltage compared to the pure electric transport.
Electrical Dynamic Simulation Activities in Forsmark NPP
International Nuclear Information System (INIS)
The original power system analysis was done in the seventies in former ASEA AB software. For approximate twenty years no major new studies was done because of limited numbers of renewal projects. In the end of the nineties the plant started to update the selectivity planning and study of the loading of the safety bus-bars. The simulation and start of the development of simulation models was done in a tool named Simpow. Simpow was also an ASEA/ABB AB software developed from the program used in the seventies. To continue to work with Simpow was a decision made after doing an extensive review of on the marked available commercially software. Also at that time we start to do our first attempt building electrical simulation models of unit 1 and 2 according to the original documentation. The development of models for the unit 1, 2 and 3 became more intensive some years after the millennium. Partly because of event July 25, 2006 and also because of the renewal of unit 1 and 2 and had subsequently been initiated for unit 3 also. Today we have initiated a conversion of our models to a new program called PowerFactory. That due to the withdrawal of support and development on SIMPOW a couple of years ago. To development relevance, accuracy and detail, models are an important issue for FKA (Forsmark Kraftgrupp AB). The model is initially created according to the plant documentation and also including requested information from the original supplier. Continued development and updates of the model is done according to the data received from the contractors via the demands according to requirements in our technical documents on different electrical components in renewal projects. The development of the model is driven by known weaknesses, depending of the type of studies and necessary data related to events. An important part that will be described is to have a verified simulation tool and validated models. An example is that the models have been validated by making start and
Computer Simulation of Turbulent Reactive Gas Dynamics
Directory of Open Access Journals (Sweden)
Bjørn H. Hjertager
1984-10-01
Full Text Available A simulation procedure capable of handling transient compressible flows involving combustion is presented. The method uses the velocity components and pressure as primary flow variables. The differential equations governing the flow are discretized by integration over control volumes. The integration is performed by application of up-wind differencing in a staggered grid system. The solution procedure is an extension of the SIMPLE-algorithm accounting for compressibility effects.
Molecular dynamics simulation of propagating cracks
Mullins, M.
1982-01-01
Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.
Dynamic Factor Method of Computing Dynamic Mathematical Model for System Simulation
Institute of Scientific and Technical Information of China (English)
老大中; 吴娟; 杨策; 蒋滋康
2003-01-01
The computational methods of a typical dynamic mathematical model that can describe the differential element and the inertial element for the system simulation are researched. The stability of numerical solutions of the dynamic mathematical model is researched. By means of theoretical analysis, the error formulas, the error sign criteria and the error relationship criterion of the implicit Euler method and the trapezoidal method are given, the dynamic factor affecting the computational accuracy has been found, the formula and the methods of computing the dynamic factor are given. The computational accuracy of the dynamic mathematical model like this can be improved by use of the dynamic factor.
Autonomous dynamic decision making in a nuclear fuel cycle simulator
International Nuclear Information System (INIS)
Highlights: • Objective criteria based decision making in a nuclear fuel cycle simulator. • Simulation driven by an evolving performance metric. • Implementation of the model in a nuclear fuel cycle simulator. • Verification of dynamic decision making based on uranium price evolution. -- Abstract: Growing energy demand and the push to move toward carbon-free ways of electricity generation have renewed the world's interest in nuclear energy. Due to the high technical and economic uncertainties related to nuclear energy, simulation tools have become a necessity in order to plan and evaluate possible nuclear fuel cycles (NFCs). Most of the NFC simulators today work by running the simulation with a user-defined set of facility build orders and preferences. While this allows for a simple way to change the simulation conditions, it may not always lead to optimal results and strongly relies on the user defining the correct parameters. This study looks into the possibility of using the expected cost of electricity (CoE) as the driving build decision variable instead of relying on user-defined build orders. This is a first step toward a more general decision making strategy in dynamic fuel cycle simulation. For this purpose, additional modules were implemented in an NFC simulator, VEGAS, with the consumption dependent price of uranium as a time-varying NFC cost component that drives the cost competitiveness of available NFC options. The model was demonstrated to verify the correct operation of a CoE-driven NFC simulator
Planar aggregation and the coalescing Brownian flow
Norris, James; Turner, Amanda
2008-01-01
We study a scaling limit associated to a model of planar aggregation. The model is obtained by composing certain independent random conformal maps. The evolution of harmonic measure on the boundary of the cluster is shown to converge to the coalescing Brownian flow.
Brownian shape motion: Fission fragment mass distributions
Sierk Arnold J.; Randrup Jørgen; Möller Peter
2012-01-01
It was recently shown that remarkably accurate fission-fragment mass distributions can be obtained by treating the nuclear shape evolution as a Brownian walk on previously calculated five-dimensional potential-energy surfaces; the current status of this novel method is described here.
Brownian coagulation at high particle concentrations
Trzeciak, T. M.
2012-01-01
The process of Brownian coagulation, whereby particles are brought together by thermal motion and grow by collisions, is one of the most fundamental processes influencing the final properties of particulate matter in a variety of technically important systems. It is of importance in colloids, emulsi
Brownian motion an introduction to stochastic processes
Schilling, René L; Böttcher, Björn
2014-01-01
Stochastic processes occur everywhere in sciences and engineering, and need to be understood by applied mathematicians, engineers and scientists alike. This is a first course introducing the reader gently to the subject. Brownian motions are a stochastic process, central to many applications and easy to treat.
Brownian shape motion: Fission fragment mass distributions
Directory of Open Access Journals (Sweden)
Sierk Arnold J.
2012-02-01
Full Text Available It was recently shown that remarkably accurate fission-fragment mass distributions can be obtained by treating the nuclear shape evolution as a Brownian walk on previously calculated five-dimensional potential-energy surfaces; the current status of this novel method is described here.
Chaos, Dissipation and Quantal Brownian Motion
Cohen, Doron
1999-01-01
Energy absorption by driven chaotic systems, the theory of energy spreading and quantal Brownian motion are considered. In particular we discuss the theory of a classical particle that interacts with quantal chaotic degrees of freedom, and try to relate it to the problem of quantal particle that interacts with an effective harmonic bath.
Scherer, Christoph
2015-01-01
Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industri...
Brownian motion of a matter-wave bright soliton moving through a thermal cloud of distinct atoms
McDonald, R. G.; Bradley, A. S.
2016-06-01
Taking an open quantum system approach, we derive a collective equation of motion for the dynamics of a matter-wave bright soliton moving through a thermal cloud of a distinct atomic species. The reservoir interaction involves energy transfer without particle transfer between the soliton and thermal cloud, thus damping the soliton motion without altering its stability against collapse. We derive a Langevin equation for the soliton center-of-mass velocity in the form of an Ornstein-Uhlenbeck process with analytical drift and diffusion coefficients. This collective motion is confirmed by simulations of the full stochastic projected Gross-Pitaevskii equation for the matter-wave field. The system offers a pathway for experimentally observing the elusive energy-damping reservoir interaction and a clear realization of collective Brownian motion for a mesoscopic superfluid droplet.
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
International Nuclear Information System (INIS)
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom
Molecular dynamics simulation of Ni3Al melting
Institute of Scientific and Technical Information of China (English)
Rongshan Wang; Huaiyu Hou; Xiaodong Ni; Guoliang Chen
2008-01-01
With the Voter-Chert version of embedded-atom model (EAM) potential and molecular dynamics, the melting of Ni3A1 alloy was simulated by one-phase (conventional) and two-phase approaches. It is shown that the simulated melting point is dependent on the potential and the simulation method. The structures of the melts obtained by different simulation methods were analyzed by the pair correlation function, the coordination number, and the distribution of atom pair type (indexed by the Honeycutt-Andersen pair analysis technique). The results show that the structures are very similar.
Numerical simulation tests with light dynamical quarks
International Nuclear Information System (INIS)
Two generate flavours of quarks are simulated with small masses down to about one fifth of the strange quark mass by using the two-step multi-boson (TSMB) algorithm. The lattice size is 83 . 16 with lattice spacing about a ≅ 0.27 fm which is not far from the Nt = 4 thermodynamical cross-over line. Autocorrelations of different physical quantities are estimated as a function of the quark mass. The eigenvalue spectra of the Wilson-Dirac operator are investigated. (orig.)
Computational fluid dynamics for sport simulation
2009-01-01
All over the world sport plays a prominent role in society: as a leisure activity for many, as an ingredient of culture, as a business and as a matter of national prestige in such major events as the World Cup in soccer or the Olympic Games. Hence, it is not surprising that science has entered the realm of sports, and, in particular, that computer simulation has become highly relevant in recent years. This is explored in this book by choosing five different sports as examples, demonstrating that computational science and engineering (CSE) can make essential contributions to research on sports topics on both the fundamental level and, eventually, by supporting athletes’ performance.
Two methods for molecular dynamics on curved surfaces
Paquay, Stefan
2014-01-01
Lateral diffusion along membranes is an important transport mechanism in biology. Dynamical simulations of this transport can greatly aid in understanding biological processes where this diffusion plays a role. Brownian dynamics simulations in local coordinates are one possibility, but we show here that it is also possible to combine constraint algorithms with a velocity Verlet scheme to perform molecular dynamics simulations of particles confined on arbitrary time-independent curved surfaces. The main advantage is that this method is based on Cartesian coordinates instead of local coordinates, allowing the reuse of many other standard tools, including parallelisation through domain decomposition, without adapting those to local coordinates. Of the two constraint algorithms we considered, RATTLE is more computationally efficient and easier to implement, while the symmetric projection method has slightly better energy conservation. By applying the schemes to the Langevin equation, Brownian motion on various cu...
New ways to boost molecular dynamics simulations.
Krieger, Elmar; Vriend, Gert
2015-05-15
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org. PMID:25824339
Distortion and flow of nematics simulated by dissipative particle dynamics
Zhao, Tongyang; Wang, Xiaogong
2014-05-01
In this study, we simulated distortion and flow of nematics by dissipative particle dynamics (DPD). The nematics were modeled by a binary mixture that contained rigid rods composed of DPD particles as mesogenic units and normal DPD particles as solvent. Elastic distortions were investigated by monitoring director orientation in space under influences of boundary anchoring and external fields. Static distortion demonstrated by the simulation is consistent with the prediction of Frank elastic theory. Spatial distortion profile of the director was examined to obtain static elastic constants. Rotational motions of the director under influence of the external field were simulated to understand the dynamic process. The rules revealed by the simulation are in a good agreement with those obtained from dynamical experiments and classical theories for nematics. Three Miesowicz viscosities were obtained by using external fields to hold the orientation of the rods in shear flows. The simulation showed that the Miesowicz viscosities have the order of ηc > ηa > ηb and the rotational viscosity γ1 is about two orders larger than the Miesowicz viscosity ηb. The DPD simulation correctly reproduced the non-monotonic concentration dependence of viscosity, which is a unique property of lyotropic nematic fluids. By comparing simulation results with classical theories for nematics and experiments, the DPD nematic fluids are proved to be a valid model to investigate the distortion and flow of lyotropic nematics.
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383
Molecular dynamics simulation of laser shock phenomena
Energy Technology Data Exchange (ETDEWEB)
Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).
2001-10-01
Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)
Magnetic-field dependence of Brownian and Néel relaxation times
Dieckhoff, Jan; Eberbeck, Dietmar; Schilling, Meinhard; Ludwig, Frank
2016-01-01
The investigation of the rotational dynamics of magnetic nanoparticles in magnetic fields is of academic interest but also important for applications such as magnetic particle imaging where the particles are exposed to magnetic fields with amplitudes of up to 25 mT. We have experimentally studied the dependence of Brownian and Néel relaxation times on ac and dc magnetic field amplitude using ac susceptibility measurements in the frequency range between 2 Hz and 9 kHz for field amplitudes up to 9 mT. As samples, single-core iron oxide nanoparticles with core diameters between 20 nm and 30 nm were used either suspended in water-glycerol mixtures or immobilized by freeze-drying. The experimentally determined relaxation times are compared with theoretical models. It was found that the Néel relaxation time decays much faster with increasing field amplitude than the Brownian one. Whereas the dependence of the Brownian relaxation time on the ac and dc field amplitude can be well explained with existing theoretical models, a proper model for the dependence of the Néel relaxation time on ac field amplitude for particles with random distribution of easy axes is still lacking. The extrapolation of the measured relaxation times of the 25 nm core diameter particles to a 25 mT ac field with an empirical model predicts that the Brownian mechanism clearly co-determines the dynamics of magnetic nanoparticles in magnetic particle imaging applications, in agreement with magnetic particle spectroscopy data.
Langevin formulation of quantum dynamics
International Nuclear Information System (INIS)
We first show that nonrelativistic quantum mechanics formulated at imaginary-(h/2 π) can formally be viewed as the Fokker-Planck description of a frictionless brownian motion, which occurs (in general) in an absorbing medium. We next offer a new formulation of quantum mechanics, which is basically the Langevin treatment of this brownian motion. Explicitly, we derive a noise-average representation for the transition probability W(X'',t''|X',t'), in terms of the solutions to a Langevin equation with a Gaussian white-noise. Upon analytic continuation back to real-(h/2 π),W(X'',t''|X',t') becomes the propagator of the original Schroedinger equation. Our approach allows for a straightforward application to quantum dynamical problems of the mathematical techniques of classical stochastic processes. Moreover, computer simulations of quantum mechanical systems can be carried out by using numerical programs based on the Langevin dynamics. (author). 19 refs, 1 tab
Robotic Simulation of Flexible-Body Spacecraft Dynamics
Brannan, Justin C.; Carignan, Craig R.
2016-01-01
A robotic testbed has been developed to conduct hardware-in-the-loop simulations of a robotic servicer interacting with a client satellite on-orbit. By creating an analytical model of a satellite with flexible appendages, it is possible to simulate the system response to external force and torque inputs and compare the predicted system motion to a robot mass simulator outfitted with physical appendages. This validation effort includes multiple test cases that encompass the types of interaction forces a satellite might experience during a nominal on-orbit servicing mission and aims to show the simulation's ability to capture the physical system response. After incorporating the flexible-body dynamics into the robotic mass simulator at NASA Goddard Space Flight Center (GSFC), a hardware-in-the-loop simulation can be used to characterize the potential impact of structural flexibility on an end-to-end satellite servicing mission.
Narrow escape for a stochastically gated Brownian ligand.
Reingruber, Jürgen; Holcman, David
2010-02-17
Molecular activation in cellular microdomains is usually characterized by a forward binding rate, which is the reciprocal of the arrival time of a ligand to a key target. Upon chemical interactions or conformational changes, a Brownian ligand may randomly switch between different states, and when target activation is possible in a specific state only, switching can significantly alter the activation process. The main goal of this paper is to study the mean time for a switching ligand to activate a small substrate, modelled as the time to exit a microdomain through a small absorbing window on the surface. We present the equations for the mean sojourn times the ligand spends in each state, and study the escape process with switching between two states in dimension one and three. When the ligand can exit in only one of the two states, we find that switching always decreases its sojourn time in the state where it can exit. Moreover, the fastest exit is obtained when the ligand diffuses most of the time in the state with the maximal diffusion coefficient, although this may imply that it spends most of the time 'hidden' in the state where it cannot exit. We discuss the physical mechanisms responsible for this apparent paradox. In dimension three we confirm our results with Brownian simulations. Finally, we suggest possible applications in cellular biology. PMID:21389363
Hybrid simulations with dynamical quarks: Spectra, screening and thermodynamics
International Nuclear Information System (INIS)
We summarize simulations made by the Argonne/University of Illinois group using the Hybrid algorithm to include dynamical staggered fermions. Recent work on the mass spectrum and screening effects due to the inclusion of four light flavors of dynamical quarks is presented. We also present a brief overview of what we have learned about the finite temperature chiral phase transition. 5 refs., 4 figs., 1 tab
Topic recipe-based social simulation for research dynamics analysis
Lee, Keeheon; Kim, Chang Ouk
2014-01-01
In this paper, we introduce an agent-based modeling and simulation model for research dynamics analysis. Since researchers constitute research systems in research dynamics, modelling the behavior of a researcher is a key to this method. A researcher makes topic recipes for research products projecting his/her interest and fulfilling financial needs under his/her capability and topical trends. A topic recipe means a combination of topics in a research field. A topic can be related to a methodo...
Micellar Crystals in Solution from Molecular Dynamics Simulations
Anderson, J A; Lorenz, C. D.; Travesset, A.
2008-01-01
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our result...
Stochastic Simulation of Cardiac Ventricular Myocyte Calcium Dynamics and Waves
Tuan, Hoang-Trong Minh; Williams, George S.B.; Chikando, Aristide C.; Sobie, Eric A.; Lederer, W. Jonathan; Jafri, M. Saleet
2011-01-01
A three dimensional model of calcium dynamics in the rat ventricular myocyte was developed to study the mechanism of calcium homeostasis and pathological calcium dynamics during calcium overload. The model contains 20,000 calcium release units (CRUs) each containing 49 ryanodine receptors. The model simulates calcium sparks with a realistic spontaneous calcium spark rate. It suggests that in addition to the calcium spark-based leak, there is an invisible calcium leak caused by the stochastic ...
Deposition of Small Clusters on Surface: a Molecular Dynamics Simulation
Institute of Scientific and Technical Information of China (English)
DUAN Xiang-Mei; GONG Xin-Gao
2000-01-01
By using the molecular dynamics simulation, we have studied the dynamic behaviors of small energetic clusters deposited on the surface. We find that, at incident energy as low as 1.0eV/atom, the structure of the cluster is destroyed and cluster atoms form an epitaxial layer above the surface. At high energy incidence, the site exchange between cluster atom and surface atom is observed. The effects of the cluster size and orientation are discussed.
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
International Nuclear Information System (INIS)
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report
Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles
Energy Technology Data Exchange (ETDEWEB)
Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire
2009-04-01
Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.
Dynamic modeling, simulation and control of energy generation
Vepa, Ranjan
2013-01-01
This book addresses the core issues involved in the dynamic modeling, simulation and control of a selection of energy systems such as gas turbines, wind turbines, fuel cells and batteries. The principles of modeling and control could be applied to other non-convention methods of energy generation such as solar energy and wave energy.A central feature of Dynamic Modeling, Simulation and Control of Energy Generation is that it brings together diverse topics in thermodynamics, fluid mechanics, heat transfer, electro-chemistry, electrical networks and electrical machines and focuses on their appli
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Coalescence of silver unidimensional structures by molecular dynamics simulation
International Nuclear Information System (INIS)
The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)
Linac Beam Dynamics Simulations With PY-ORBIT
International Nuclear Information System (INIS)
Linac dynamics simulation capabilities of the PyORBIT code are discussed. PyORBIT is an open source code and a further development of the original ORBIT code that was created and used for design, studies, and commissioning of the SNS ring. The PyORBIT code, like the original one, has a two-layer structure. C++ is used to perform time-consuming computations, and the program flow is controlled from a Python language shell. The flexible structure makes it possible to use PyORBIT also for linac dynamics simulations. A benchmark of PyORBIT with Parmila and the XAL Online model is presented.
Neutron Scattering and Computer Simulation Studies of Ice Dynamics
Institute of Scientific and Technical Information of China (English)
DONG Shunle; YU Xinsheng
2002-01-01
In this article we describe a range of simulations (lattice dynamics and molecular dynamics) of the inelastic inco-herent neutron scattering spectra of ices (normal ice, ice Ⅱ and ice Ⅷ ). These simulations use a variety of different inter-molecular potentials from simple classic pair-wise (rigid and non-rigid molecule) potentials to sophisticated polarisable poten-tials. It was found that MCY makes stretching and bending interactions too weak while others do them well. We demon-strate that in order to reproduce the measured neutron spectrum, greater anisotropy (or orientational variation) is requiredthan these potentials presently provide.
Simulation of Dynamic Recrystallization Using Cellular Automaton Method
Institute of Scientific and Technical Information of China (English)
XIAO Hong; XIE Hong-biao; YAN Yan-hong; Jun YANAGIMOTO
2004-01-01
A new modeling approach that couples fundamental metallurgical principles of dynamical recrystallization with the cellular automaton method was developed to simulate the microstructural evolution linking with the plastic flow behavior during thermomechanical processing. The driving force for the nucleation and growth of dynamically recrystallized grain is the volume free energy due to the stored dislocation density of a deformation matrix. The growth terminates the impingement. The model is capable of simulating kinetics, microstructure and texture evolution during recrystallization. The predictions of microstructural evolution agree with the experimental results.
Simulation of dynamic behavior of unanchored tanks
International Nuclear Information System (INIS)
Evaluation of the commonly used seismic design procedures for unanchored liquid storage tanks has shown that current standards are inconsistent in predicting the behavior of these structures. In general, the estimation of liquid-exerted overturning moments lacks explicit consideration of the support effects. The overturning moment caused by the hydrodynamic pressure tends to lift the shell off its foundation which may cause buckling of the shell on one side and a separation of the base plate from the shell on the other, thereby releasing the tank contents. A finite element program capable of handling the complexities associated with the nonlinear dynamic response of unanchored tanks was developed. It was observed that the overturning moment exerted on an unanchored tank may be smaller than that exerted on a similar anchored tank, yet the stresses at the shell bottom of an unanchored tank shell are generally much larger than those of an anchored tank subjected to the same ground motion. (author). 5 refs., 5 figs., 1 tab
Simulation of Stir Casting Process Using Computational Fluid Dynamics
M. V. S. Pavan Kumar; M. V. Sekhar Babu
2015-01-01
Stir casting process is one of the methods to produce Metal Matrix Composites (MMCs). But the Particle Distribution of Non-Homogenous material is the greatest problem facing now days to produce MMCs. The present simulations were conducted how the speed of the stirrer effects the Particle Distribution of NonHomogenous material. The Simulations were performed using Computational Fluid Dynamics. In this experiment Copper is used as Semi Solid Metal (SSM) and Silicon-Carbide is used a...
Mathematical Model to Simulate Tuberculosis Disease Population Dynamics
Directory of Open Access Journals (Sweden)
O. K. Koriko
2008-01-01
Full Text Available A mathematical model to depict Tuberculosis disease population dynamics was presented. The model population was compartmentalised as appropriate and the resulting model equations were solved numerically while different instances of the disease transmission were simulated. The graphical profiles of the various sub-populations with time were presented and discussed based on the results from our simulations. Also, the disease-free and endemic equilibrium of the system were established and analyzed for stability.
Dynamic Simulation of Household Refrigerators: Numerical Model and Experimental Comparison
Ablanque, Nicolas; Oliet, Carles; Rigola, Joaquim; Lehmkuhl, Oriol; Oliva, Assensi
2014-01-01
This work presents a dynamic model to simulate a whole household refrigeration unit taking into account both the refrigeration cycle itself and the refrigerated compartments network. The methodology implemented to achieve the transient simulation of the whole system combines a steady-state approach for the refrigerating cycle loop with a transient approach for the refrigerated compartments loop. Both loops are solved at each time step (the linking boundary conditions for the refrigerating cyc...
Modelling and simulation of landing dynamics for a space vehicle
Tejedor Fontanet, Ramon
2008-01-01
The purpose of this study is to examine the feasibility of using Monte Carlo simulation applied in the procedure to facilitate the simulation of landing dynamics at the touchdown moment. Historically, the designers and mission planners were more interested in getting to Mars with a functioning vehicle than in reaching a particular geographic location. Nowadays, when the landing conditions are “met” becomes more important the study of the touchdown moment. This report is d...
Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit
Xu, Ji; Ren, Ying; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai
2010-01-01
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 ar...
Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins
Fogolari, Federico; Brigo, Alessandro; Molinari, Henriette
2003-01-01
Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poi...
Hydration of polyelectrolytes studied by molecular dynamics simulation
Biermann, Oliver; Haedicke, Erich; Koltzenburg, Sebastian; Seufert, Michael; Mueller-Plathe, Florian
2001-01-01
Molecular dynamics simulations of diluted (~2.5 weight percent) aqueous solutions of two polyelectrolytes, namely sodium carboxy methyl cellulose (CMC) and sodium poly(acrylate) (PAA) have been performed. Water and counterions were taken into account explicitly. For CMC the substitution pattern and starting conformation is all-important. Two simulations of CMC oligomers resulted in different structures: One molecule takes a stretched conformation, while the second one keeps a globule-like, to...
Error and efficiency of replica exchange molecular dynamics simulations.
Rosta, Edina; Hummer, Gerhard
2009-10-28
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977
Molecular Dynamics Simulations of Protein Dynamics and their relevance to drug discovery
Salsbury, Freddie R.
2010-01-01
Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery.
Predicting population dynamics with analytical, simulation and supercomputer models
Energy Technology Data Exchange (ETDEWEB)
Onstad, D.W.
1987-07-01
A set of epizootiological models describing the influence of a microsporidian disease on the population dynamics of an herbivorous insect demonstrate the similarities and differences between the three major approaches now available for ecological modeling. Simulation modeling allows the incorporation of randomness or the timing of discrete events in the temporal dynamics. More complex models incorporating both temporal and spatial dynamics in variable and heterogeneous environments require the use of supercomputers. Under a number of realistic circumstances, the qualitative predictions of the approaches may differ.
Stability of molecular dynamics simulations of classical systems
DEFF Research Database (Denmark)
Toxværd, Søren
2012-01-01
The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives...
Modelling and simulation of dynamic characteristics of CANDU-SCWR
International Nuclear Information System (INIS)
Owing to the thermal properties of supercritical water and features of heat transfer correlation under supercritical pressure, a detailed thermal-hydraulic model with movable boundary of is developed for CANDU-SCWR (Supercritical Water-Cooled Reactor). Steady-state results of the model agree well with the design data. The dynamic responses of CANDU-SCWR to different disturbances are simulated and characteristics are analyzed. A dynamic model for ACR is also developed using CATHENA. Differences between dynamic characteristics of CANDU-SCWR and those of ACR are highlighted and investigated. It is concluded that CANDU-SCWR has a larger time constant, but with a higher response amplitude. (author)
Marshall, Deborah A.; Burgos-Liz, Lina; IJzerman, M.J.; Crown, William; Padula, William V.; Wong, Peter K.; Pasupathy, Kalyan S.; Higashi, Mitchell K.; Osgood, Nathaniel D.
2015-01-01
In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling c
Developments of multibody system dynamics: computer simulations and experiments
International Nuclear Information System (INIS)
It is an exceptional success when multibody dynamics researchers Multibody System Dynamics journal one of the most highly ranked journals in the last 10 years. In the inaugural issue, Professor Schiehlen wrote an interesting article explaining the roots and perspectives of multibody system dynamics. Professor Shabana also wrote an interesting article to review developments in flexible multibody dynamics. The application possibilities of multibody system dynamics have grown wider and deeper, with many application examples being introduced with multibody techniques in the past 10 years. In this paper, the development of multibody dynamics is briefly reviewed and several applications of multibody dynamics are described according to the author's research results. Simulation examples are compared to physical experiments, which show reasonableness and accuracy of the multibody formulation applied to real problems. Computer simulations using the absolute nodal coordinate formulation (ANCF) were also compared to physical experiments; therefore, the validity of ANCF for large-displacement and large-deformation problems was shown. Physical experiments for large deformation problems include beam, plate, chain, and strip. Other research topics currently being carried out in the author's laboratory are also briefly explained
Molecular dynamics simulations of oscillatory flows in microfluidic channels
DEFF Research Database (Denmark)
Hansen, J.S.; Ottesen, Johnny T.
2006-01-01
In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system with...
Simulations of boundary migration during recrystallization using molecular dynamics
DEFF Research Database (Denmark)
Godiksen, Rasmus Brauner; Trautt, Z.T.; Upmanyu, M.;
2007-01-01
We have applied an atomistic simulation methodology based on molecular dynamics to study grain boundary migration in crystalline materials, driven by the excess energy of dislocation arrangements. This method is used to simulate recrystallization in metals. The simulations reveal that the migration...... process is not uniform as assumed in many recrystallization models, but that the grain boundaries migrate in an irregular fashion and exhibit a strong dependence on the local presence of dislocations, which can distort the local migration process significantly. (c) 2007 Acta Materialia Inc. Published...
Structural and Dynamic Properties of Amorphous Silicon:Tight-Binding Molecular Dynamics Simulation
Institute of Scientific and Technical Information of China (English)
HUANG Shi-Ping; WANG Wen-Chuan
2004-01-01
@@ The tight-binding molecular dynamics simulation has been performed to study structural and dynamical properties of amorphous silicon. It is found that the radial distribution function and static structure factor are in good agreement with the experimental measurements. The bond order parameters Ql are sensitive to the structure change at different quenching rates. For the dynamical properties, we have calculated the vibration and electronic density of states. The simulation results show that the transverse acoustic is in good agreement with the experimental data, and the high frequency transverse optical (TO) peak shifts to the right of the experimental TO peak.
From Lagrangian to Brownian motion
International Nuclear Information System (INIS)
We present a Lagrangian describing an idealized liquid interacting with a particle immersed in it. We show that the equation describing the motion of the particle as a functional of the initial conditions of the liquid incorporates noise and friction, which are attributed to specific dynamical processes. The equation is approximated to yield a Langevin equation with parameters depending on the Lagrangian and the temperature of the liquid. The origin of irreversibility and dissipation is discussed
Optimization of hydrogen vehicle refueling via dynamic simulation
DEFF Research Database (Denmark)
Rothuizen, Erasmus Damgaard; Mérida, W.; Rokni, Masoud;
2013-01-01
A dynamic model has been developed to analyze and optimize the thermodynamics and design of hydrogen refueling stations. The model is based on Dymola software and incorporates discrete components. Two refueling station designs were simulated and compared. The modeling results indicate that pressu...
THE REFINEMENT OF NMR STRUCTURES BY MOLECULAR-DYNAMICS SIMULATION
TORDA, AE; VANGUNSTEREN, WF
1991-01-01
We discuss the use of molecular dynamics simulations as a tool for the refinement of structures based on NMR data. The procedure always involves the construction of a pseudo-energy term to model the experimental data and we consider the various approaches to this problem. We detail recent work where
Simulation of dynamics of a permanent magnet linear actuator
DEFF Research Database (Denmark)
Yatchev, Ivan; Ritchie, Ewen
2010-01-01
Comparison of two approaches for the simulation of the dynamic behaviour of a permanent magnet linear actuator is presented. These are full coupled model, where the electromagnetic field, electric circuit and mechanical motion problems are solved simultaneously, and decoupled model, where first a...
Simulating Poverty and Inequality Dynamics in Developing Countries
Ansoms, An; Geenen, Sara
2012-01-01
This article considers how the simulation game of DEVELOPMENT MONOPOLY provides insight into poverty and inequality dynamics in a development context. It first discusses how the game is rooted in theoretical and conceptual frameworks on poverty and inequality. Subsequently, it reflects on selected playing experiences, with special focus on the…
Molecular Dynamics Simulations Study on Chiral Room -Temperature Ionic Liquids
Czech Academy of Sciences Publication Activity Database
Lísal, Martin; Chvál, Z.; Storch, Jan; Izák, Pavel; Aim, Karel
Frankfurt : DECHEMA, 2012, P2-35. ISBN N. [European Symposium on Applied Thermodynamics - ESAT 2012 /26./. Potsdam (DE), 07.10.2012-10.10.2012] Institutional support: RVO:67985858 Keywords : ionic liquids * molecular dynamics simulations * thermodynamics properties Subject RIV: CF - Physical ; Theoretical Chemistry http://events.dechema.de/events/en/esat2012.html
Dynamic simulation of thermal-lag Stirling engines
International Nuclear Information System (INIS)
Highlights: • First paper dealing with numerical dynamic simulation of thermal-lag Stirling engine. • Observation on different operating modes, such as rotating, swinging, swinging-to-rotate, and swinging-to-decay modes. • Study of influential factors affecting the operating modes. • Optimal geometrical or operating parameters of the baseline case for maximum engine power are found. - Abstract: The present study is concerned with dynamic simulation of thermal-lag Stirling engines. A dynamic model is built and incorporated with a thermodynamic model to study the engine start process. A prototype engine is designed and simulated by using the dynamic model. In the simulation, different operating modes, including rotating mode, swinging mode, swinging-to-rotate mode, and swinging-to-decay mode, have been observed. The rotating mode is desired and can be achieved if the operating parameters are properly designed. In a poor design, the engine may switch to the swinging or even the swinging-to-decay mode. In addition, it is found that geometric parameters, such as bore size, stroke, and volume of working spaces, also determine the operating mode of the engine. Brake thermal efficiency of the engine is monotonically reduced by increasing engine speed. However, study of the dependence of the shaft power of the engine speed shows that there exists a maximum value of the shaft power at an optimal operating engine speed. The optimal engine speed leading to maximum shaft power is significantly influenced by the geometrical parameters
Molecular dynamics simulations on PGLa using NMR orientational constraints
International Nuclear Information System (INIS)
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide
Molecular dynamics simulations on PGLa using NMR orientational constraints
Energy Technology Data Exchange (ETDEWEB)
Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)
2015-11-15
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.
A new simulation algorithm for lattice QCD with dynamical quarks
Bunk, B.; Jansen, K.; Jegerlehner, B.; Lüscher, M.; Simma, H.; Sommer, R
1994-01-01
A previously introduced multi-boson technique for the simulation of QCD with dynamical quarks is described and some results of first test runs on a $6^3\\times12$ lattice with Wilson quarks and gauge group SU(2) are reported.
Molecular dynamics simulation of the Ni(001) surface
Energy Technology Data Exchange (ETDEWEB)
Chirita, V.; Pailthorpe, B.A. (School of Physics, Univ. of Sydney, New South Wales (Australia))
1992-02-10
A Lennard-Jones two-body interatomic potential is used in a molecular dynamics simulation of bulk nickel and of the Ni(001) surface stabilized using a Dion-Barker-Merrill substrate interaction. It is found that the bulk and surface Debye temperatures and surface atomic displacements compare well with previous theoretical and experimental studies. (orig.).
Molecular dynamics simulation of a charged biological membrane
López Cascales, J.J.; García de la Torre, J.; Marrink, S.J.; Berendsen, H.J.C.
1996-01-01
A molecular dynamics simulation of a membrane with net charge in its liquid-crystalline state was carried out. It was modeled by dipalmitoylphosphatidylserine lipids with net charge, sodium ions as counterions and water molecules. The behavior of this membrane differs from that was shown by other me
Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit
Xu, Ji; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai
2010-01-01
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 spee...
Brownian Thermal Noise in Multilayer Coated Mirrors
Hong, Ting; Gustafson, Eric K; Adhikari, Rana X; Chen, Yanbei
2012-01-01
We analyze the Brownian thermal noise of a multi-layer dielectric coating, used in high-precision optical measurements including interferometric gravitational-wave detectors. We assume the coating material to be isotropic, and therefore study thermal noises arising from shear and bulk losses of the coating materials. We show that coating noise arises not only from layer thickness fluctuations, but also from fluctuations of the interface between the coating and substrate, driven by internal fluctuating stresses of the coating. In addition, the non-zero photoeleastic coefficients of the thin films modifies the influence of the thermal noise on the laser field. The thickness fluctuations of different layers are statistically independent, however, there exists a finite coherence between layers and the substrate-coating interface. Taking into account uncertainties in material parameters, we show that significant uncertainties still exist in estimating coating Brownian noise.
Modeling an efficient Brownian heat engine
Asfaw, Mesfin
2008-09-01
We discuss the effect of subdividing the ratchet potential on the performance of a tiny Brownian heat engine that is modeled as a Brownian particle hopping in a viscous medium in a sawtooth potential (with or without load) assisted by alternately placed hot and cold heat baths along its path. We show that the velocity, the efficiency and the coefficient of performance of the refrigerator maximize when the sawtooth potential is subdivided into series of smaller connected barrier series. When the engine operates quasistatically, we analytically show that the efficiency of the engine can not approach the Carnot efficiency and, the coefficient of performance of the refrigerator is always less than the Carnot refrigerator due to the irreversible heat flow via the kinetic energy.
Brownian motion, martingales, and stochastic calculus
Le Gall, Jean-François
2016-01-01
This book offers a rigorous and self-contained presentation of stochastic integration and stochastic calculus within the general framework of continuous semimartingales. The main tools of stochastic calculus, including Itô’s formula, the optional stopping theorem and Girsanov’s theorem, are treated in detail alongside many illustrative examples. The book also contains an introduction to Markov processes, with applications to solutions of stochastic differential equations and to connections between Brownian motion and partial differential equations. The theory of local times of semimartingales is discussed in the last chapter. Since its invention by Itô, stochastic calculus has proven to be one of the most important techniques of modern probability theory, and has been used in the most recent theoretical advances as well as in applications to other fields such as mathematical finance. Brownian Motion, Martingales, and Stochastic Calculus provides a strong theoretical background to the reader interested i...
Brownian thermal noise in multilayer coated mirrors
Hong, Ting; Yang, Huan; Gustafson, Eric K.; Adhikari, Rana X.; Chen, Yanbei
2013-04-01
We analyze the Brownian thermal noise of a multilayer dielectric coating used in high-precision optical measurements, including interferometric gravitational-wave detectors. We assume the coating material to be isotropic, and therefore study thermal noises arising from shear and bulk losses of the coating materials. We show that coating noise arises not only from layer thickness fluctuations, but also from fluctuations of the interface between the coating and substrate, driven by fluctuating shear stresses of the coating. Although thickness fluctuations of different layers are statistically independent, there exists a finite coherence between the layers and the substrate-coating interface. In addition, photoelastic coefficients of the thin layers (so far not accurately measured) further influence the thermal noise, although at a relatively low level. Taking into account uncertainties in material parameters, we show that significant uncertainties still exist in estimating coating Brownian noise.
Dynamic simulation for effective workforce management in new product development
Directory of Open Access Journals (Sweden)
M. Mutingi
2012-10-01
Full Text Available Effective planning and management of workforce for new product development (NPD projects is a great challenge to many organisations, especially in the presence of engineering changes during the product development process. The management objective in effective workforce management is to recruit, develop and deploy the right people at the right place at the right time so as to fulfill organizational objectives. In this paper, we propose a dynamic simulation model to address the workforce management problem in a typical NPD project consisting of design, prototyping, and production phases. We assume that workforce demand is a function of project work remaining and the current available skill pool. System dynamics simulation concepts are used to capture the causality relationships and feedback loops in the workforce system from a systems thinking. The evaluation of system dynamics simulation reveals the dynamic behaviour in NPD workforce management systems and shows how adaptive dynamic recruitment and training decisions can effectively balance the workforce system during the NPD process.
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
International Nuclear Information System (INIS)
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)
2015-12-07
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
Molecular dynamics simulations of Pd-Ni transition metal alloys
International Nuclear Information System (INIS)
Molecular Dynamics simulations are performed to study bulk properties of fcc metals and metal alloys by using the quantum Sutton-Chen many-body potentials within the context of the tight-binding approach. The Molecular Dynamics algorithms we used in the simulations of Pd-Ni alloys are based on an extended Hamiltonian formalism arising from the works of Andersen (1980), Parinello and Rahman (1980), Nose (1984), Hoover (1985) and Cagin (1988). In these simulations, the effect of temperature and concentration on the solid and liquid properties are studied. Elastic constants and phonon dispersion relation are the solid properties we simulated in this work. Dynamic and static properties of liquid Pd-Ni are also computed by examining the behavior of density, enthalpy, pair distribution function and structure factor. The melting temperatures of Pd-Ni alloys are investigated. The diffusion coefficients are calculated from the mean square displacement using Einstein relation and from velocity auto-correlation function using Green-Kubo relations. The simulation results are in good agreement with the experiments
Brownian coagulation at high particle concentrations
Trzeciak, T. M.
2012-01-01
The process of Brownian coagulation, whereby particles are brought together by thermal motion and grow by collisions, is one of the most fundamental processes influencing the final properties of particulate matter in a variety of technically important systems. It is of importance in colloids, emulsions, flocculation, air pollution, soot formation, materials manufacture and growth of interstellar dust, to name a few of its applications. With continuous progress in particulate matter processing...
The quantum brownian particle and memory effects
International Nuclear Information System (INIS)
The Quantum Brownian particle, immersed in a heat bath, is described by a statistical operator whose evolution is ruled by a Generalized Master Equation (GME). The heat bath degrees of freedom are considered to be either white noise or coloured noise correlated,while the GME is considered under either the Markov or Non-Markov approaches. The comparison between these considerations are fully developed and their physical meaning is discussed. (author)
Steered molecular dynamics simulations of protein-ligand interactions
Institute of Scientific and Technical Information of China (English)
XU Yechun; SHEN Jianhua; LUO Xiaomin; SHEN Xu; CHEN Kaixian; JIANG Hualiang
2004-01-01
Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APA from HIV-1 reverse transcriptase.
Molecular dynamics simulations of detonation on the roadrunner supercomputer
Mniszewski, Susan; Cawkwell, Marc; Germann, Timothy C.
2012-03-01
The temporal and spatial scales intrinsic to a real detonating explosive are extremely difficult to capture using molecular dynamics (MD) simulations. Nevertheless, MD remains very attractive since it allows for the resolution of dynamic phenomena at the atomic scale. Large-scale reactive MD simulations in three dimensions require immense computational resources even when simple reactive force fields are employed. We focus on the REBO force field for 'AB' since it has been shown to support a detonation while being simple, analytic, and short-ranged. The transition from two-to three- dimensional simulations is being facilitated by the port of the REBO force field in the parallel MD code SPaSM to LANL's petaflop supercomputer 'Roadrunner'. We provide a detailed discussion of the challenges associated with computing interatomic forces on a hybrid Opteron/Cell BE computational architecture.
Software life cycle dynamic simulation model: The organizational performance submodel
Tausworthe, Robert C.
1985-01-01
The submodel structure of a software life cycle dynamic simulation model is described. The software process is divided into seven phases, each with product, staff, and funding flows. The model is subdivided into an organizational response submodel, a management submodel, a management influence interface, and a model analyst interface. The concentration here is on the organizational response model, which simulates the performance characteristics of a software development subject to external and internal influences. These influences emanate from two sources: the model analyst interface, which configures the model to simulate the response of an implementing organization subject to its own internal influences, and the management submodel that exerts external dynamic control over the production process. A complete characterization is given of the organizational response submodel in the form of parameterized differential equations governing product, staffing, and funding levels. The parameter values and functions are allocated to the two interfaces.
Ultrascale simulations of non-smooth granular dynamics
Preclik, Tobias; Rüde, Ulrich
2015-06-01
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their micro-dynamics and thus to extend the time and length scales that can be simulated. The global multi-contact problem is solved using a non-linear block Gauss-Seidel method that is conforming to the subdomain structure. The parallel algorithms employ a sophisticated protocol between processors that delegate algorithmic tasks such as contact treatment and position integration uniquely and robustly to the processors. Communication overhead is minimized through aggressive message aggregation, leading to excellent strong and weak scaling. The robustness and scalability is assessed on three clusters including two peta-scale supercomputers with up to 458,752 processor cores. The simulations can reach unprecedented resolution of up to ten billion () non-spherical particles and contacts.
Haptization of molecular dynamics simulation with thermal display
International Nuclear Information System (INIS)
Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)
Quantum simulation of the dynamical Casimir effect with trapped ions
Trautmann, N.; Hauke, P.
2016-04-01
Quantum vacuum fluctuations are a direct manifestation of Heisenberg’s uncertainty principle. The dynamical Casimir effect (DCE) allows for the observation of these vacuum fluctuations by turning them into real, observable photons. However, the observation of this effect in a cavity QED experiment would require the rapid variation of the length of a cavity with relativistic velocities, a daunting challenge. Here, we propose a quantum simulation of the DCE using an ion chain confined in a segmented ion trap. We derive a discrete model that enables us to map the dynamics of the multimode radiation field inside a variable-length cavity to radial phonons of the ion crystal. We perform a numerical study comparing the ion-chain quantum simulation under realistic experimental parameters to an ideal Fabry–Perot cavity, demonstrating the viability of the mapping. The proposed quantum simulator, therefore, allows for probing the photon (respectively phonon) production caused by the DCE on the single photon level.
Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin
Energy Technology Data Exchange (ETDEWEB)
Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)
1994-12-31
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
Ultrascale Simulations of Non-smooth Granular Dynamics
Preclik, Tobias
2015-01-01
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their micro-dynamics and thus to extend the time and length scales that can be simulated. The multi-contact problem is solved using a non-linear block Gauss-Seidel method that is conforming to the subdomain structure. The parallel algorithms employ a sophisticated protocol between processors that delegate algorithmic tasks such as contact treatment and position integration uniquely and robustly to the processors. Communication overhead is minimized through aggressive message aggregation, leading to excellent strong and weak scaling. The robustness and scalability is assessed on three clusters including two peta-scale supercomputers with up to 458752 processor cores. The simulations can reach unprecedented resolution of up to ten billion non-spherical particles and contacts.
Parallel alternating direction preconditioner for isogeometric simulations of explicit dynamics
Łoś, Marcin
2015-04-27
In this paper we present a parallel implementation of the alternating direction preconditioner for isogeometric simulations of explicit dynamics. The Alternating Direction Implicit (ADI) algorithm, belongs to the category of matrix-splitting iterative methods, was proposed almost six decades ago for solving parabolic and elliptic partial differential equations, see [1–4]. The new version of this algorithm has been recently developed for isogeometric simulations of two dimensional explicit dynamics [5] and steady-state diffusion equations with orthotropic heterogenous coefficients [6]. In this paper we present a parallel version of the alternating direction implicit algorithm for three dimensional simulations. The algorithm has been incorporated as a part of PETIGA an isogeometric framework [7] build on top of PETSc [8]. We show the scalability of the parallel algorithm on STAMPEDE linux cluster up to 10,000 processors, as well as the convergence rate of the PCG solver with ADI algorithm as preconditioner.
ParaDiS-FEM dislocation dynamics simulation code primer
International Nuclear Information System (INIS)
The ParaDiS code is developed to study bulk systems with periodic boundary conditions. When we try to perform discrete dislocation dynamics simulations for finite systems such as thin films or cylinders, the ParaDiS code must be extended. First, dislocations need to be contained inside the finite simulation box; Second, dislocations inside the finite box experience image stresses due to the free surfaces. We have developed in-house FEM subroutines to couple with the ParaDiS code to deal with free surface related issues in the dislocation dynamics simulations. This primer explains how the coupled code was developed, the main changes from the ParaDiS code, and the functions of the new FEM subroutines.
ParaDiS-FEM dislocation dynamics simulation code primer
Energy Technology Data Exchange (ETDEWEB)
Tang, M; Hommes, G; Aubry, S; Arsenlis, A
2011-09-27
The ParaDiS code is developed to study bulk systems with periodic boundary conditions. When we try to perform discrete dislocation dynamics simulations for finite systems such as thin films or cylinders, the ParaDiS code must be extended. First, dislocations need to be contained inside the finite simulation box; Second, dislocations inside the finite box experience image stresses due to the free surfaces. We have developed in-house FEM subroutines to couple with the ParaDiS code to deal with free surface related issues in the dislocation dynamics simulations. This primer explains how the coupled code was developed, the main changes from the ParaDiS code, and the functions of the new FEM subroutines.
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519
Optimum analysis of a Brownian refrigerator.
Luo, X G; Liu, N; He, J Z
2013-02-01
A Brownian refrigerator with the cold and hot reservoirs alternating along a space coordinate is established. The heat flux couples with the movement of the Brownian particles due to an external force in the spatially asymmetric but periodic potential. After using the Arrhenius factor to describe the behaviors of the forward and backward jumps of the particles, the expressions for coefficient of performance (COP) and cooling rate are derived analytically. Then, through maximizing the product of conversion efficiency and heat flux flowing out, a new upper bound only depending on the temperature ratio of the cold and hot reservoirs is found numerically in the reversible situation, and it is a little larger than the so-called Curzon and Ahlborn COP ε(CA)=(1/√[1-τ])-1. After considering the irreversible factor owing to the kinetic energy change of the moving particles, we find the optimized COP is smaller than ε(CA) and the external force even does negative work on the Brownian particles when they jump from a cold to hot reservoir. PMID:23496491
Information Diversity in Structure and Dynamics of Simulated Neuronal Networks
Directory of Open Access Journals (Sweden)
Tuomo eMäki-Marttunen
2011-06-01
Full Text Available Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance (NCD. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess diﬀering path length and clustering coeﬃcient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using diﬀerent network structures and their bursting behaviours are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses.We show that the structure of the simulated neuronal networks aﬀects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.