Hybrid simulations of lateral diffusion in fluctuating membranes

In this paper we introduce a novel method to simulate lateral diffusion of inclusions in a fluctuating membrane. The regarded systems are governed by two dynamic processes: the height fluctuations of the membrane and the diffusion of the inclusion along the membrane. While membrane fluctuations can be expressed in terms of a dynamic equation which follows from the Helfrich Hamiltonian, the dynamics of the diffusing particle is described by a Langevin or Smoluchowski equation. In the latter equations, the curvature of the surface needs to be accounted for, which makes particle diffusion a function of membrane fluctuations. In our scheme these coupled dynamic equations, the membrane equation and the Langevin equation for the particle, are numerically integrated to simulate diffusion in a membrane. The simulations are used to study the ratio of the diffusion coefficient projected on a flat plane and the intramembrane diffusion coefficient for the case of free diffusion. We compare our results with recent analytical results that employ a preaveraging approximation and analyze the validity of this approximation. A detailed simulation study of the relevant correlation functions reveals a surprisingly large range where the approximation is applicable.Comment: 12 pages, 9 figures, accepted for publication in Phys. Rev.

Curvature-coupling dependence of membrane protein diffusion coefficients

We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature of the particle. We employ stochastic simulations that take into account both the thermal fluctuations of the membrane and the diffusive behavior of the particle. In this study we neglect the influence of the particle on the membrane dynamics, thus the membrane dynamics agrees with that of a freely fluctuating membrane. Overall, we find that this curvature-coupling substantially enhances the diffusion coefficient. We compare the ratio of the projected or measured diffusion coefficient and the free intramembrane diffusion coefficient, which is a parameter of the simulations, with analytical results that rely on several approximations. We find that the simulations always lead to a somewhat smaller diffusion coefficient than our analytical approach. A detailed study of the correlations of the forces acting on the particle indicates that the diffusing inclusion tries to follow favorable positions on the membrane, such that forces along the trajectory are on average smaller than they would be for random particle positions.Comment: 16 pages, 8 figure

Mobile Robotics Activities in DOE Laboratories

This paper will briefly outline major activities in Department of Energy (DOE) Laboratories focused on mobile platforms, both Unmanned Ground Vehicles (UGV’s) as well as Unmanned Air Vehicles (UAV’s). The activities will be discussed in the context of the science and technology construct used by the DOE Technology Roadmap for Robotics and Intelligent Machines (RIM)1 published in 1998; namely, Perception, Reasoning, Action, and Integration. The activities to be discussed span from research and development to deployment in field operations. The activities support customers in other agencies. The discussion of "perception" will include hyperspectral sensors, complex patterns discrimination, multisensor fusion and advances in LADAR technologies, including real-world perception. "Reasoning" activities to be covered include cooperative controls, distributed systems, ad-hoc networks, platform-centric intelligence, and adaptable communications. The paper will discuss "action" activities such as advanced mobility and various air and ground platforms. In the RIM construct, "integration" includes the Human-Machine Integration. Accordingly the paper will discuss adjustable autonomy and the collaboration of operator(s) with distributed UGV’s and UAV’s. Integration also refers to the applications of these technologies into systems to perform operations such as perimeter surveillance, large-area monitoring and reconnaissance. Unique facilities and test beds for advanced mobile systems will be described. Given that this paper is an overview, rather than delve into specific detail in these activities, other more exhaustive references and sources will be cited extensively

Curvature correction to the mobility of fluid membrane inclusions

For the first time, using rigorous low-Reynolds-number hydrodynamic theory on curved surfaces via a Stokeslet-type approach, we provide a general and concise expression for the leading-order curvature correction to the canonical, planar, Saffman-Delbrück value of the diffusion constant for a small inclusion embedded in an arbitrarily (albeit weakly) curved fluid membrane. In order to demonstrate the efficacy and utility of this wholly general result, we apply our theory to the specific case of calculating the diffusion coefficient of a locally curvature inducing membrane inclusion. By including both the effects of inclusion and membrane elasticity, as well as their respective thermal shape fluctuations, excellent agreement is found with recently published experimental data on the surface tension dependent mobility of membrane bound inclusions

Spinodal Decomposition in a Binary Polymer Mixture: Dynamic Self Consistent Field Theory and Monte Carlo Simulations

We investigate how the dynamics of a single chain influences the kinetics of early stage phase separation in a symmetric binary polymer mixture. We consider quenches from the disordered phase into the region of spinodal instability. On a mean field level we approach this problem with two methods: a dynamical extension of the self consistent field theory for Gaussian chains, with the density variables evolving in time, and the method of the external potential dynamics where the effective external fields are propagated in time. Different wave vector dependencies of the kinetic coefficient are taken into account. These early stages of spinodal decomposition are also studied through Monte Carlo simulations employing the bond fluctuation model that maps the chains -- in our case with 64 effective segments -- on a coarse grained lattice. The results obtained through self consistent field calculations and Monte Carlo simulations can be compared because the time, length, and temperature scales are mapped onto each other through the diffusion constant, the chain extension, and the energy of mixing. The quantitative comparison of the relaxation rate of the global structure factor shows that a kinetic coefficient according to the Rouse model gives a much better agreement than a local, i.e. wave vector independent, kinetic factor. Including fluctuations in the self consistent field calculations leads to a shorter time span of spinodal behaviour and a reduction of the relaxation rate for smaller wave vectors and prevents the relaxation rate from becoming negative for larger values of the wave vector. This is also in agreement with the simulation results.Comment: Phys.Rev.E in prin

SystemBurn: Principles of Design and Operation Release 3.0

As high performance computing technology progresses toward the progressively more extreme scales required to address critical computational problems of both national and global interest, power and cooling for these extreme scale systems is becoming a growing concern. A standardized methodology for testing system requirements under maximal system load and validating system environmental capability to meet those requirements is critical to maintaining system stability and minimizing power and cooling risks for high end data centers. Moreover, accurate testing permits the high end data center to avoid issues of under- or over-provisioning power and cooling capacity saving resources and mitigating hazards. Previous approaches to such testing have employed an ad hoc collection of tools, which have been anecdotally perceived to produce a heavy system load. In this report, we present SystemBurn, a software tool engineered to allow a system user to methodically create a maximal system load on large scale systems for the purposes of testing and validation

SystemBurn: Principles of Design and Operation, Release 2.0

As high performance computing technology progresses toward the progressively more extreme scales required to address critical computational problems of both national and global interest, power and cooling for these extreme scale systems is becoming a growing concern. A standardized methodology for testing system requirements under maximal system load and validating system environmental capability to meet those requirements is critical to maintaining system stability and minimizing power and cooling risks for high end data centers. Moreover, accurate testing permits the high end data center to avoid issues of under- or over-provisioning power and cooling capacity saving resources and mitigating hazards. Previous approaches to such testing have employed an ad hoc collection of tools, which have been anecdotally perceived to produce a heavy system load. In this report, we present SystemBurn, a software tool engineered to allow a system user to methodically create a maximal system load on large scale systems for the purposes of testing and validation

Fiskalische Kosten einer steuerlichen Förderung von Forschung und Entwicklung in Deutschland - Eine empirische Analyse verschiedener Gestaltungsoptionen

Der Beitrag berechnet die Aufkommensausfälle verschiedener Gestaltungsmodelle für eine steuerliche Forschungsförderung in Deutschland auf Basis eines Mikrosimulationsmodells. Die fiskalischen Kosten betragen zwischen 464 Mio. € und 5.701 Mio. €. Eine Erstattungsoption der Steuergutschrift über die Gewerbe- und Körperschaftsteuerschuld hinaus ist unerlässlich, da sonst etwa ein Drittel der Unternehmen nicht oder nur teilweise in den Genuss der Förderung kommen würde und sich dadurch starke Verzerrungen zwischen ertragsstarken und ertragsschwachen Unternehmen ergeben. Eine Differenzierung der Fördersätze für KMU und große Unternehmen kann die Aufkommensausfälle wirksam begrenzen. Eine Kappungsgrenze in Höhe eines absoluten Betrages ist wegen der Verzerrungen innerhalb der Gruppe großer Unternehmen ungünstig. Als besonders pragmatisch erscheint eine Verrechnung der Steuergutschrift mit der abzuführenden Lohnsteuer

Model of SNARE-Mediated Membrane Adhesion Kinetics

SNARE proteins are conserved components of the core fusion machinery driving diverse membrane adhesion and fusion processes in the cell. In many cases micron-sized membranes adhere over large areas before fusion. Reconstituted in vitro assays have helped isolate SNARE mechanisms in small membrane adhesion-fusion and are emerging as powerful tools to study large membrane systems by use of giant unilamellar vesicles (GUVs). Here we model SNARE-mediated adhesion kinetics in SNARE-reconstituted GUV-GUV or GUV-supported bilayer experiments. Adhesion involves many SNAREs whose complexation pulls apposing membranes into contact. The contact region is a tightly bound rapidly expanding patch whose growth velocity increases with SNARE density . We find three patch expansion regimes: slow, intermediate, fast. Typical experiments belong to the fast regime where depends on SNARE diffusivities and complexation binding constant. The model predicts growth velocities s. The patch may provide a close contact region where SNAREs can trigger fusion. Extending the model to a simple description of fusion, a broad distribution of fusion times is predicted. Increasing SNARE density accelerates fusion by boosting the patch growth velocity, thereby providing more complexes to participate in fusion. This quantifies the notion of SNAREs as dual adhesion-fusion agents