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Sample records for brownian interacting molecule

  1. 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.

  2. Particle diode: Rectification of interacting Brownian ratchets

    OpenAIRE

    Ai, Bao-quan; He, Ya-feng; Zhong, Wei-rong

    2012-01-01

    Transport of Brownian particles interacting with each other via the Morse potential is investigated in the presence of an ac driving force applied locally at one end of the chain. By using numerical simulations, we find that the system can behave as a particle diode for both overdamped and underdamped cases. For low frequencies, the transport from the free end to the ac acting end is prohibited, while the transport from the ac acting end to the free end is permitted. However, the polarity of ...

  3. Entropic Ratchet transport of interacting active Brownian particles

    International Nuclear Information System (INIS)

    Ai, Bao-Quan; He, Ya-Feng; Zhong, Wei-Rong

    2014-01-01

    Directed transport of interacting active (self-propelled) Brownian particles is numerically investigated in confined geometries (entropic barriers). The self-propelled velocity can break thermodynamical equilibrium and induce the directed transport. It is found that the interaction between active particles can greatly affect the ratchet transport. For attractive particles, on increasing the interaction strength, the average velocity first decreases to its minima, then increases, and finally decreases to zero. For repulsive particles, when the interaction is very weak, there exists a critical interaction at which the average velocity is minimal, nearly tends to zero, however, for the strong interaction, the average velocity is independent of the interaction

  4. Conserved linear dynamics of single-molecule Brownian motion

    Science.gov (United States)

    Serag, Maged F.; Habuchi, Satoshi

    2017-06-01

    Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.

  5. Conserved linear dynamics of single-molecule Brownian motion

    KAUST Repository

    Serag, Maged F.

    2017-06-06

    Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.

  6. Efficiency of interacting Brownian motors: Improved mean-field treatment

    Czech Academy of Sciences Publication Activity Database

    Slanina, František

    2009-01-01

    Roč. 135, 5-6 (2009), s. 935-950 ISSN 0022-4715 R&D Projects: GA ČR GA202/07/0404 Institutional research plan: CEZ:AV0Z10100520 Keywords : Brownian motors * diffusion Subject RIV: BE - Theoretical Physics Impact factor: 1.390, year: 2009 http://www.springerlink.com/content/1040451k48528058/?p=9aa7761fe82743b69f9feafc3a665c0cπ=1

  7. Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

    Science.gov (United States)

    Butler, Jason E.; Shaqfeh, Eric S. G.

    2005-01-01

    Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

  8. The Kardar-Parisi-Zhang Equation as Scaling Limit of Weakly Asymmetric Interacting Brownian Motions

    Science.gov (United States)

    Diehl, Joscha; Gubinelli, Massimiliano; Perkowski, Nicolas

    2017-09-01

    We consider a system of infinitely many interacting Brownian motions that models the height of a one-dimensional interface between two bulk phases. We prove that the large scale fluctuations of the system are well approximated by the solution to the KPZ equation provided the microscopic interaction is weakly asymmetric. The proof is based on the martingale solutions of Gonçalves and Jara (Arch Ration Mech Anal 212(2):597-644, 2014) and the corresponding uniqueness result of Gubinelli and Perkowski (Energy solutions of KPZ are unique, 2015).

  9. Electron-excited molecule interactions

    International Nuclear Information System (INIS)

    Christophorou, L.G.; Tennessee Univ., Knoxville, TN

    1991-01-01

    In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10 6 to 10 7 times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs

  10. Diffusion mechanism of non-interacting Brownian particles through a deformed substrate

    Science.gov (United States)

    Arfa, Lahcen; Ouahmane, Mehdi; El Arroum, Lahcen

    2018-02-01

    We study the diffusion mechanism of non-interacting Brownian particles through a deformed substrate. The study is done at low temperature for different values of the friction. The deformed substrate is represented by a periodic Remoissenet-Peyrard potential with deformability parameter s. In this potential, the particles (impurity, adatoms…) can diffuse. We ignore the interactions between these mobile particles consider them merely as non-interacting Brownian particles and this system is described by a Fokker-Planck equation. We solve this equation numerically using the matrix continued fraction method to calculate the dynamic structure factor S(q , ω) . From S(q , ω) some relevant correlation functions are also calculated. In particular, we determine the half-width line λ(q) of the peak of the quasi-elastic dynamic structure factor S(q , ω) and the diffusion coefficient D. Our numerical results show that the diffusion mechanism is described, depending on the structure of the potential, either by a simple jump diffusion process with jump length close to the lattice constant a or by a combination of a jump diffusion model with jump length close to lattice constant a and a liquid-like motion inside the unit cell. It shows also that, for different friction regimes and various potential shapes, the friction attenuates the diffusion mechanism. It is found that, in the high friction regime, the diffusion process is more important through a deformed substrate than through a non-deformed one.

  11. Correlational approach to study interactions between dust Brownian particles in a plasma

    Science.gov (United States)

    Lisin, E. A.; Vaulina, O. S.; Petrov, O. F.

    2018-01-01

    A general approach to the correlational analysis of Brownian motion of strongly coupled particles in open dissipative systems is described. This approach can be applied to the theoretical description of various non-ideal statistically equilibrium systems (including non-Hamiltonian systems), as well as for the analysis of experimental data. In this paper, we consider an application of the correlational approach to the problem of experimental exploring the wake-mediated nonreciprocal interactions in complex plasmas. We derive simple analytic equations, which allows one to calculate the gradients of forces acting on a microparticle due to each of other particles as well as the gradients of external field, knowing only the information on time-averaged correlations of particles displacements and velocities. We show the importance of taking dissipative and random processes into account, without which consideration of a system with a nonreciprocal interparticle interaction as linearly coupled oscillators leads to significant errors in determining the characteristic frequencies in a system. In the examples of numerical simulations, we demonstrate that the proposed original approach could be an effective instrument in exploring the longitudinal wake structure of a microparticle in a plasma. Unlike the previous attempts to study the wake-mediated interactions in complex plasmas, our method does not require any external perturbations and is based on Brownian motion analysis only.

  12. Random walks, Brownian motion, and interacting particle systems: a festschrift in honor of Frank Spitzer

    National Research Council Canada - National Science Library

    Durrett, Richard; Kesten, Harry; Spitzer, Frank

    1991-01-01

    ..., made the transparency used in the printing process. STUDENTS OF FRANK SPITZERSTUDENTS OF FRANK SPITZER 1957 J. W. Lamperti, On the asymptotic behavior of recurrent and almostrecurrent events. 1964 W. W. Whitman, Some strong laws for random walks and Brownian motion. 1965 J. C. Mineka, The existence and uniqueness of positive solutions to the Wien...

  13. Electron-molecule interactions and their applications

    CERN Document Server

    Christophorou, L G

    1984-01-01

    Electron-Molecule Interactions and Their Applications, Volume 2 provides a balanced and comprehensive account of electron-molecule interactions in dilute and dense gases and liquid media. This book consists of six chapters. Chapter 1 deals with electron transfer reactions, while Chapter 2 discusses electron-molecular positive-ion recombination. The electron motion in high-pressure gases and electron-molecule interactions from single- to multiple-collision conditions is deliberated in Chapter 3. In Chapter 4, knowledge on electron-molecule interactions in gases is linked to that on similar proc

  14. Hydrodynamically Coupled Brownian Dynamics: A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions

    Science.gov (United States)

    Ahuja, V. R.; van der Gucht, J.; Briels, W. J.

    2018-01-01

    We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different

  15. Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

    Science.gov (United States)

    Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

    Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.

  16. Parallel O(N) Stokes' solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries

    Science.gov (United States)

    Zhao, Xujun; Li, Jiyuan; Jiang, Xikai; Karpeev, Dmitry; Heinonen, Olle; Smith, Barry; Hernandez-Ortiz, Juan P.; de Pablo, Juan J.

    2017-06-01

    An efficient parallel Stokes' solver has been developed for complete description of hydrodynamic interactions between Brownian particles in bulk and confined geometries. A Langevin description of the particle dynamics is adopted, where the long-range interactions are included using a Green's function formalism. A scalable parallel computational approach is presented, where the general geometry Stokeslet is calculated following a matrix-free algorithm using the general geometry Ewald-like method. Our approach employs a highly efficient iterative finite-element Stokes' solver for the accurate treatment of long-range hydrodynamic interactions in arbitrary confined geometries. A combination of mid-point time integration of the Brownian stochastic differential equation, the parallel Stokes' solver, and a Chebyshev polynomial approximation for the fluctuation-dissipation theorem leads to an O(N) parallel algorithm. We illustrate the new algorithm in the context of the dynamics of confined polymer solutions under equilibrium and non-equilibrium conditions. The method is then extended to treat suspended finite size particles of arbitrary shape in any geometry using an immersed boundary approach.

  17. Modelling of energetic molecule-surface interactions

    International Nuclear Information System (INIS)

    Kerford, M.

    2000-09-01

    This thesis contains the results of molecular dynamics simulations of molecule-surface interactions, looking particularly at fullerene molecules and carbon surfaces. Energetic impacts of fullerene molecules on graphite create defect craters. The relationship between the parameters of the impacting molecule and the parameters of the crater axe examined and found to be a function of the energy and velocity of the impacting molecule. Less energetic fullerene molecules can be scattered from a graphite surface and the partitioning of energy after a scattering event is investigated. It is found that a large fraction of the kinetic energy retained after impact is translational energy, with a small fraction of rotational energy and a number of vibrational modes. At impact energies where the surface is not broken and at normal incidence, surface waves axe seen to occur. These waves axe used to develop a method of desorbing molecules from a graphite surface without damage to either the surface or the molecules being desorbed. A number of fullerene molecules are investigated and ways to increase the desorption yield are examined. It is found that this is a successful technique for desorbing large numbers of intact molecules from graphite. This technique could be used for desorbing intact molecules into a gas phase for mass spectrometric analysis. (author)

  18. Charged molecular films on brownian particles: structure, interactions, and relation to stability.

    Science.gov (United States)

    Zaccone, Alessio; Wu, Hua; Lattuada, Marco; Morbidelli, Massimo

    2008-06-05

    The interfacial film of physically adsorbed ionic amphiphilic molecules on submicron particles dispersed in water was studied by a combination of surface tension measurements, laser light scattering (LLS) and high-shear experiments in a microchannel. General features in the structure and morphology of the molecular film are identified and understood in the framework of the two-step Langmuir adsorption model deduced from the adsorption isotherm. On the basis of this approach, the phase transitions and structural ordering of the film at the solid-liquid interface are analyzed in detail. A novel methodology based on high-shear aggregation experiments subsequently analyzed by means of LLS is proposed and turns out to be able to provide significant information on the phase transitions and structural arrangements of the adsorbed molecules (in substantial agreement with the adsorption isotherm model) as well as on the resulting interactions. Particularly important for applications is the result that, with no added salt, the films on two particles can adhere/fuse, leading to aggregation as long as an uncovered (hydrophobic) patch is present (unsaturated molecular layers). In the opposite case of fully developed layers, by analyzing the mechanism of shear aggregation of charged particles in the low-salt limit, we show that, when the hydrophobic attraction is absent, short-range hydration repulsive forces dominate over Derjaguin-Landau-Verwey-Overbeek (DLVO) forces and adhesion can never be achieved even upon application of very high collision energies. Consistently, a lower limiting boundary for the hydration interaction is calculated and found to be in agreement with data in the literature.

  19. The Interactions Between Nitrogen and Oxygen Molecules

    Science.gov (United States)

    Meador, Willard E., Jr.

    1960-01-01

    Lippincott's delta-function model for atomic interactions is analyzed, both physically and mathematically, and extended, by differentiation between K- and L-shell electrons and the introduction of a variable parameter in the expression for the delta-function strength, to cover homonuclear molecules more complex than hydrogen. In addition, modifications are made which allow treatments of diatomic, heteronuclear molecules. This theory, in conjunction with a reasonably extensive study of resonance, dispersion, and configuration interaction phenomena, as well as the use of simple quantum mechanical arguments, is then applied to the N2-N2, N2-O2, and O2-O2 interactions.

  20. Interactions of electrons with biologically important molecules

    International Nuclear Information System (INIS)

    Pisklova, K.; Papp, P.; Stano, M.

    2012-01-01

    For the study of interactions of low-energy electrons with the molecules in the gas phase, the authors used electron-molecule cross-beam apparatus. The experiment is carried out in high vacuum, where molecules of the tested compound are inducted through a capillary. For purposes of this experiment the sample was electrically heated to 180 Deg C., giving a bundle of GlyGly molecules into the gas phase. The resulting signals can be evaluated in two different modes: mass spectrum - at continuous electron energy (e.g. 100 eV) they obtained the signal of intensity of the ions according to their mass to charge ratio; ionization and resonance spectra - for selected ion mass when the authors received the signal of intensity of the ions, depending on the energy of interacting electron.

  1. Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

    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.

  2. Short-range interaction between hydrogen molecules

    Science.gov (United States)

    Mcmahan, A. K.; Beck, H.; Krumhansl, J. A.

    1974-01-01

    Recent calculations of the ground state energy of a system of four hydrogen atoms are reviewed with the aim of discerning the short-range repulsive part of the interaction potential between two hydrogen molecules. Extended-basis CI calculations which include a diffuse 2p orbital appear to be capable of determining the total interaction energy between to hydrogen molecules for any separation. Consistent results of such calculations suggest that the potential for intermolecular separations in the region from 1 to 2.5 A can now be specified to better than 10% with considerable confidence. Analytic fits to spherical averages of these results are presented.

  3. Optimized green fluorescent protein fused to FoF1-ATP synthase for single-molecule FRET using a fast anti-Brownian electrokinetic trap

    Science.gov (United States)

    Dienerowitz, Maria; Ilchenko, Mykhailo; Su, Bertram; Deckers-Hebestreit, Gabriele; Mayer, Günter; Henkel, Thomas; Heitkamp, Thomas; Börsch, Michael

    2016-02-01

    Observation times of freely diffusing single molecules in solution are limited by the photophysics of the attached fluorescence markers and by a small observation volume in the femtolitre range that is required for a sufficient signal-to-background ratio. To extend diffusion-limited observation times through a confocal detection volume, A. E. Cohen and W. E. Moerner have invented and built the ABELtrap -- a microfluidic device to actively counteract Brownian motion of single nanoparticles with an electrokinetic trap. Here we present a version of an ABELtrap with a laser focus pattern generated by electro-optical beam deflectors and controlled by a programmable FPGA chip. This ABELtrap holds single fluorescent nanoparticles for more than 100 seconds, increasing the observation time of fluorescent nanoparticles compared to free diffusion by a factor of 10000. To monitor conformational changes of individual membrane proteins in real time, we record sequential distance changes between two specifically attached dyes using Förster resonance energy transfer (smFRET). Fusing the a-subunit of the FoF1-ATP synthase with mNeonGreen results in an improved signal-to-background ratio at lower laser excitation powers. This increases our measured trap duration of proteoliposomes beyond 2 s. Additionally, we observe different smFRET levels attributed to varying distances between the FRET donor (mNeonGreen) and acceptor (Alexa568) fluorophore attached at the a- and c-subunit of the FoF1-ATP synthase respectively.

  4. Bonding and interaction of molecules with surfaces

    International Nuclear Information System (INIS)

    Ellis, D.E.

    1988-01-01

    In this lecture it is intended to discuss some general features of bonding and interaction of molecules with surfaces. The geometry of surface complexes is sufficiently difficult and the interaction mechanisms are sufficiently subtle. That all possible theoretical models need to be exploited such as: i) Semiempirical - including Huckel molecular orbital theory; ii)first principles including self-consistent-field Hartree-Fock and Local Density approaches; iii)explicitly correlated, including C.I., Generalized Valence Bond, Coupled Cluster Perturbation Theory and Many Body Perturbation Theory. (A.C.A.S.) [pt

  5. Single-Molecule Imaging of GPCR Interactions.

    Science.gov (United States)

    Calebiro, Davide; Sungkaworn, Titiwat

    2018-02-01

    G protein-coupled receptors (GPCRs) constitute the largest family of membrane receptors and are of great interest as pharmacological targets. Although the occurrence of GPCR signaling nanodomains has long been hypothesized based on indirect evidence, this and other fundamental aspects of GPCR signaling have been difficult to prove. The advent of single-molecule microscopy methods, which allow direct visualization of individual membrane proteins with unprecedented spatiotemporal resolution, provides unique opportunities to address several of these open questions. Indeed, recent single-molecule studies have revealed that GPCRs and G proteins transiently interact with each other as well as with structural components of the plasma membrane, leading to the formation of dynamic complexes and 'hot spots' for GPCR signaling. Whereas we are only beginning to understand the implications of this unexpected level of complexity, single-molecule approaches are likely to play a crucial role to further dissect the protein-protein interactions that are at the heart of GPCR signaling. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Simple Brownian diffusion an introduction to the standard theoretical models

    CERN Document Server

    Gillespie, Daniel T

    2013-01-01

    Brownian diffusion, the motion of large molecules in a sea of very many much smaller molecules, is topical because it is one of the ways in which biologically important molecules move about inside living cells. This book presents the mathematical physics that underlies the four simplest models of Brownian diffusion.

  7. Single-molecule magnets ``without'' intermolecular interactions

    Science.gov (United States)

    Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.

    2012-02-01

    Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).

  8. Structure formation in bis(terpyridine) derivative adlayers: molecule-substrate versus molecule-molecule interactions.

    Science.gov (United States)

    Hoster, Harry E; Roos, Matthias; Breitruck, Achim; Meier, Christoph; Tonigold, Katrin; Waldmann, Thomas; Ziener, Ulrich; Landfester, Katharina; Behm, R Jürgen

    2007-11-06

    The influence of the substrate and the deposition conditions-vapor deposition versus deposition from solution-on the structures formed upon self-assembly of deposited bis(terpyridine) derivative (2,4'-BTP) monolayers on different hexagonal substrates, including highly oriented pyrolytic graphite (HOPG), Au(111), and (111)-oriented Ag thin films, was investigated by high-resolution scanning tunneling microscopy and by model calculations of the intermolecular energies and the lateral corrugation of the substrate-adsorbate interaction. Similar quasi-quadratic network structures with almost the same lattice constants obtained on all substrates are essentially identical to the optimum configuration expected from an optimization of the adlayer structure with C-H...N-type bridging bonds as a structure-determining factor, which underlines a key role of the intermolecular interactions in adlayer order. Slight distortions from the optimum values to form commensurate adlayer structures on the metal substrates and the preferential orientation of the adlayer with respect to the substrate are attributed to the substrate-adsorbate interactions, specifically, the lateral corrugation in the substrate-adsorbate interaction upon lateral displacement and rotation of the adsorbed BTP molecules. The fact that similar adlayer structures are obtained on HOPG under ultrahigh vacuum conditions (solid|gas interface) and on HOPG in trichlorobenzene (solid|liquid interface) indicates that the intermolecular interactions are not severely affected by the solvent.

  9. Random motion and Brownian rotation

    International Nuclear Information System (INIS)

    Wyllie, G.

    1980-01-01

    The course is centred on the Brownian motion - the random movement of molecules arising from thermal fluctuations of the surrounding medium - and starts with the classical theory of A. Einstein, M.v. Smoluchowski and P. Langevin. The first part of this article is quite elementary, and several of the questions raised in it have been instructively treated in a much more sophisticated way in recent reviews by Pomeau and Resibois and by Fox. This simple material may nevertheless be helpful to some readers whose main interest lies in approaching the work on Brownian rotation reviewed in the latter part of the present article. The simplest, and most brutally idealised, problem in our field of interest is that of the random walk in one dimension of space. Its solution leads on, through the diffusivity-mobility relation of Einstein, to Langevin's treatment of the Brownian motion. The application of these ideas to the movement of a molecule in a medium of similar molecules is clearly unrealistic, and much energy has been devoted to finding a suitable generalisation. We shall discuss in particular ideas due to Green, Zwanzig and Mori. (orig./WL)

  10. Interaction of ultrashort pulses with molecules and solids: Physics ...

    Indian Academy of Sciences (India)

    2014-07-26

    energy materials. Abstract. The interaction of ultrashort laser pulses with molecules and solids is an extremely complex area of science research encompassing the fields of physics, chemistry, and materials science. The physics ...

  11. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  12. Microenvironment Influences Interaction of Signaling Molecules | Center for Cancer Research

    Science.gov (United States)

    Tumor progression depends not only on events that occur within cancer cells but also on the interaction of cancer cells with their environment, which can regulate tumor growth and metastasis and modulate the formation of new blood vessels to nourish the tumor. All cells communicate with other cells around them, including endothelial cells (the cells that make up blood vessels). They also interact with the extracellular matrix (ECM), a network of sugars and proteins that supports cells. Communication between neighboring cells and molecules often occurs through interaction among and between molecules on the cell surface and molecules of the ECM. Defining these interactions should facilitate the development of novel approaches to limit tumor progression.

  13. Brownian Agents and Active Particles: Collective Dynamics in the Natural and Social Sciences

    International Nuclear Information System (INIS)

    McKane, Alan

    2003-01-01

    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

  14. Interactions Between Ground-State Nitrogen Atoms and Molecules

    Science.gov (United States)

    Vanderslice, Joseph T.; Mason, Edward A.; Lippincott, Ellis R.

    1959-01-01

    Potential-energy curves for nitrogen atom (N-N) interactions corresponding to the X (1)Sigma(sup +, sub g), A (3)Sigma(sup +, sub u), (5)Sigma(sup +, sub g), (7)Sigma(sup +, sub u), B (3) Pi(sub g), C (3)(Pi(su u)and a (1)Pi(sub g) states of the nitrogen molecule N2 as well as curves for the atom-molecules (N-N2) and molecule-molecule (N2-N2) interactions have been calculated. All calculations have been based as nearly as possible on experimental data, including spectroscopically determined vibrational energy levels, scattering cross sections of atomic beams in gases, and measured vibrational relaxation times. In cases where experimental data were not available, approximate quantum-mechanical calculations have been made. Results obtained by these various methods are remarkably consistent with one another and are believed to have good accuracy.

  15. Stabilization of protein-protein interaction complexes through small molecules.

    Science.gov (United States)

    Zarzycka, Barbara; Kuenemann, Mélaine A; Miteva, Maria A; Nicolaes, Gerry A F; Vriend, Gert; Sperandio, Olivier

    2016-01-01

    Most of the small molecules that have been identified thus far to modulate protein-protein interactions (PPIs) are inhibitors. Another promising way to interfere with PPI-associated biological processes is to promote PPI stabilization. Even though PPI stabilizers are still scarce, stabilization of PPIs by small molecules is gaining momentum and offers new pharmacological options. Therefore, we have performed a literature survey of PPI stabilization using small molecules. From this, we propose a classification of PPI stabilizers based on their binding mode and the architecture of the complex to facilitate the structure-based design of stabilizers. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Visualizing Chemical Interaction Dynamics of Confined DNA Molecules

    Science.gov (United States)

    Henkin, Gilead; Berard, Daniel; Stabile, Frank; Leslie, Sabrina

    We present a novel nanofluidic approach to controllably introducing reagent molecules to interact with confined biopolymers and visualizing the reaction dynamics in real time. By dynamically deforming a flow cell using CLiC (Convex Lens-induced Confinement) microscopy, we are able to tune reaction chamber dimensions from micrometer to nanometer scales. We apply this gentle deformation to load and extend DNA polymers within embedded nanotopographies and visualize their interactions with other molecules in solution. Quantifying the change in configuration of polymers within embedded nanotopographies in response to binding/unbinding of reagent molecules provides new insights into their consequent change in physical properties. CLiC technology enables an ultra sensitive, massively parallel biochemical analysis platform which can acces a broader range of interaction parameters than existing devices.

  17. Electrical autonomous Brownian gyrator

    Science.gov (United States)

    Chiang, K.-H.; Lee, C.-L.; Lai, P.-Y.; Chen, Y.-F.

    2017-09-01

    We study experimentally and theoretically the steady-state dynamics of a simple stochastic electronic system featuring two resistor-capacitor circuits coupled by a third capacitor. The resistors are subject to thermal noises at real temperatures. The voltage fluctuation across each resistor can be compared to a one-dimensional Brownian motion. However, the collective dynamical behavior, when the resistors are subject to distinct thermal baths, is identical to that of a Brownian gyrator, as first proposed by Filliger and Reimann [Phys. Rev. Lett. 99, 230602 (2007), 10.1103/PhysRevLett.99.230602]. The average gyrating dynamics is originated from the absence of detailed balance due to unequal thermal baths. We look into the details of this stochastic gyrating dynamics, its dependences on the temperature difference and coupling strength, and the mechanism of heat transfer through this simple electronic circuit. Our work affirms the general principle and the possibility of a Brownian ratchet working near room temperature scale.

  18. Interaction of aromatic molecules with small gold clusters

    Science.gov (United States)

    Molina, Luis M.; López, María. J.; Alonso, Julio A.

    2017-09-01

    Ab initio density functional simulations have been performed to study the adsorption of aromatic molecules (benzene and toluene) on small Aun clusters. The calculations reveal a strong interaction between gold and π electrons of benzene, accompanied by a small electronic charge transfer from benzene to gold. We report a variety of binding conformations, with varying degrees of contact between the carbon atoms in benzene and the cluster. Therefore, the interaction between the aromatic part of molecules involved in the synthesis of fine chemicals catalyzed by gold must not be neglected, and could play an important role during some reaction stages.

  19. Reciprocal carbonyl-carbonyl interactions in small molecules and proteins.

    Science.gov (United States)

    Rahim, Abdur; Saha, Pinaki; Jha, Kunal Kumar; Sukumar, Nagamani; Sarma, Bani Kanta

    2017-07-19

    Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a "reciprocal" carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.Carbonyl-carbonyl π* non covalent interactions affect the structure and stability of small molecules and proteins. Here, the authors carry out experimental studies, analyses of crystallographic databases and theoretical calculations to describe an additional type of carbonyl-carbonyl interaction.

  20. Simulating electric field interactions with polar molecules using spectroscopic databases.

    Science.gov (United States)

    Owens, Alec; Zak, Emil J; Chubb, Katy L; Yurchenko, Sergei N; Tennyson, Jonathan; Yachmenev, Andrey

    2017-03-24

    Ro-vibrational Stark-associated phenomena of small polyatomic molecules are modelled using extensive spectroscopic data generated as part of the ExoMol project. The external field Hamiltonian is built from the computed ro-vibrational line list of the molecule in question. The Hamiltonian we propose is general and suitable for any polar molecule in the presence of an electric field. By exploiting precomputed data, the often prohibitively expensive computations associated with high accuracy simulations of molecule-field interactions are avoided. Applications to strong terahertz field-induced ro-vibrational dynamics of PH 3 and NH 3 , and spontaneous emission data for optoelectrical Sisyphus cooling of H 2 CO and CH 3 Cl are discussed.

  1. Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Riley, Kevin Eugene; Hobza, Pavel

    2012-01-01

    Roč. 8, č. 11 (2012), s. 4285-4292 ISSN 1549-9618 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : halogenated molecules * noncovalent interactions * benchmark calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.389, year: 2012

  2. Interaction of ultrashort pulses with molecules and solids: Physics ...

    Indian Academy of Sciences (India)

    of photonics, lithography, biomedicine, sensing, telecommunications etc. In the present article we describe three different components of interaction of ultrashort pulses with matter: (1) with liquid molecules/thin films wherein we present the results from our studies of optical nonlinearities pre- dominantly using picosecond ...

  3. Static structure of active Brownian hard disks

    Science.gov (United States)

    de Macedo Biniossek, N.; Löwen, H.; Voigtmann, Th; Smallenburg, F.

    2018-02-01

    We explore the changes in static structure of a two-dimensional system of active Brownian particles (ABP) with hard-disk interactions, using event-driven Brownian dynamics simulations. In particular, the effect of the self-propulsion velocity and the rotational diffusivity on the orientationally-averaged fluid structure factor is discussed. Typically activity increases structural ordering and generates a structure factor peak at zero wave vector which is a precursor of motility-induced phase separation. Our results provide reference data to test future statistical theories for the fluid structure of active Brownian systems. This manuscript was submitted for the special issue of the Journal of Physics: Condensed Matter associated with the Liquid Matter Conference 2017.

  4. Efficiency of Brownian Motors

    OpenAIRE

    Parrondo, J. M. R.; Blanco, J. M.; Cao, F. J.; Brito, R.

    1998-01-01

    The efficiency of different types of Brownian motors is calculated analytically and numerically. We find that motors based on flashing ratchets present a,low efficiency and an unavoidable entropy production. On the other hand, a certain class of motors based on adiabatically changing potentials, named reversible ratchets, exhibit a higher efficiency and the entropy production can be arbitrarily reduced.

  5. Brownian motion of tethered nanowires.

    Science.gov (United States)

    Ota, Sadao; Li, Tongcang; Li, Yimin; Ye, Ziliang; Labno, Anna; Yin, Xiaobo; Alam, Mohammad-Reza; Zhang, Xiang

    2014-05-01

    Brownian motion of slender particles near a boundary is ubiquitous in biological systems and in nanomaterial assembly, but the complex hydrodynamic interaction in those systems is still poorly understood. Here, we report experimental and computational studies of the Brownian motion of silicon nanowires tethered on a substrate. An optical interference method enabled direct observation of microscopic rotations of the slender bodies in three dimensions with high angular and temporal resolutions. This quantitative observation revealed anisotropic and angle-dependent hydrodynamic wall effects: rotational diffusivity in inclined and azimuth directions follows different power laws as a function of the length, ∼ L(-2.5) and ∼ L(-3), respectively, and is more hindered for smaller inclined angles. In parallel, we developed an implicit simulation technique that takes the complex wire-wall hydrodynamic interactions into account efficiently, the result of which agreed well with the experimentally observed angle-dependent diffusion. The demonstrated techniques provide a platform for studying the microrheology of soft condensed matters, such as colloidal and biological systems near interfaces, and exploring the optimal self-assembly conditions of nanostructures.

  6. Modulation of intermolecular interactions in single-molecule magnets

    Science.gov (United States)

    Heroux, Katie Jeanne

    Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including

  7. Detecting single DNA molecule interactions with optical microcavities (Presentation Recording)

    Science.gov (United States)

    Vollmer, Frank

    2015-09-01

    Detecting molecules and their interactions lies at the heart of all biosensor devices, which have important applications in health, environmental monitoring and biomedicine. Achieving biosensing capability at the single molecule level is, moreover, a particularly important goal since single molecule biosensors would not only operate at the ultimate detection limit by resolving individual molecular interactions, but they could also monitor biomolecular properties which are otherwise obscured in ensemble measurements. For example, a single molecule biosensor could resolve the fleeting interaction kinetics between a molecule and its receptor, with immediate applications in clinical diagnostics. We have now developed a label-free biosensing platform that is capable of monitoring single DNA molecules and their interaction kinetics[1], hence achieving an unprecedented sensitivity in the optical domain, Figure 1. We resolve the specific contacts between complementary oligonucleotides, thereby detecting DNA strands with less than 2.4 kDa molecular weight. Furthermore we can discern strands with single nucleotide mismatches by monitoring their interaction kinetics. Our device utilizes small glass microspheres as optical transducers[1,2, 3], which are capable of increasing the number of interactions between a light beam and analyte molecules. A prism is used to couple the light beam into the microsphere. Ourr biosensing approach resolves the specific interaction kinetics between single DNA fragments. The optical transducer is assembled in a simple three-step protocol, and consists of a gold nanorod attached to a glass microsphere, where the surface of the nanorod is further modified with oligonucleotide receptors. The interaction kinetics of an oligonucleotide receptor with DNA fragments in the surrounding aqueous solution is monitored at the single molecule level[1]. The light remains confined inside the sphere where it is guided by total internal reflections along a

  8. Determination of lateral interactions between NO molecules on Rh(111)

    International Nuclear Information System (INIS)

    Hagelaar, J H A; Flipse, C F J; Jansen, A P J

    2007-01-01

    In this study, the STM was used to locally study the adsorption of NO on a Rh(111) single crystal. Three new structures were identified. At 200 K, patches of the (4 x 2)-2NO and an unreported (2 x 2)-2NO structure were found at about 0.50ML coverage. Higher exposure gave rise to a (2 x 2)-3NO structure with all molecules adsorbed in the hcp sites. At 5K, a (4 x 4)-1NO structure was observed. The large separation between the molecules can only arise from repulsive interactions over a distance of at least four times the lattice constant (11 A). Here the interaction is estimated to be of the order of ∼10K or ∼0.1 kJ/mol. Dynamic Monte Carlo simulations taking into account adsorption, diffusion and pairwise interactions between adsorbates were used to fit the lateral interaction for the next-next nearest neighbor to the patched STM topograph at 200K for 0.50ML coverage. The value was determined to be 2 kJ/mol. Using pairwise interactions only (2 x 2)-3NO structure could not be explained. It might therefore be necessary to include three-particle interactions. Recent DFT calculations support this idea by showing attractive three-particle interactions

  9. Thermophoresis of a Brownian particle driven by inhomogeneous thermal fluctuation

    Science.gov (United States)

    Tsuji, Tetsuro; Saita, Sho; Kawano, Satoyuki

    2018-03-01

    Brownian motion of a spherical particle induced by the interaction with surrounding molecules is considered. If the particle is larger than the molecules and the temperature of surrounding media is spatially non-uniform, the interaction between an individual molecule and the particle is also position-dependent. That is, the particle is subject to inhomogeneous thermal fluctuation. In this paper, we investigate the contribution of the inhomogeneous thermal fluctuation to the thermophoresis, i.e., the Soret coefficient or thermal diffusion factor. The problem is simplified by assuming a hard-sphere potential between the particle and the surrounding molecules and is investigated using the kinetic theory, namely, we consider a linear Boltzmann-type equation for the velocity distribution function of the particle. Using the perturbation analysis with respect to the square root of mass ratio between the molecule and the particle, the drift-diffusion equation of the particle is derived. It is found that the Soret coefficient, or thermal diffusion factor, is dependent on the mass ratio and the excluded volume of the particle. In particular, when the ratio of the mass density of the particle to that of the surrounding media decreases, the Soret coefficient also decreases and may take negative value. The present result well describes the mass-dependency of thermal diffusion factor obtained by the molecular dynamics simulation carried out in an existing study and the one in the present study, where soft potentials of Lennard-Jones-type are used instead of hard-sphere potential.

  10. NK receptor interactions with MHC class I molecules in pregnancy.

    Science.gov (United States)

    Trowsdale, John; Moffett, Ashley

    2008-12-01

    Both HLA class I molecules and their receptors on Natural Killer cells, the KIR molecules, are highly polymorphic. It is generally believed that this variation is driven in response to the role of these receptors and counter-receptors in resistance to disease. Uterine NK cells are the major maternal leukocyte population present within the decidua, and they express KIR2D receptors for HLA-C, the only polymorphic class I molecule on trophoblast. Genetic and functional data suggest that the maternal KIR/fetal HLA-C interaction in pregnancy may affect the delivery of an optimal blood supply to mother and fetus. The drive for novelty in HLA-C and KIR2D allelic diversity may relate not only to survival from infections but also to reproductive success.

  11. Low-energy positron interactions with atoms and molecules

    International Nuclear Information System (INIS)

    Surko, C M; Gribakin, G F; Buckman, S J

    2005-01-01

    This paper is a review of low-energy positron interactions with atoms and molecules. Processes of interest include elastic scattering, electronic and vibrational excitation, ionization, positronium formation and annihilation. An overview is presented of the currently available theoretical and experimental techniques to study these phenomena, including the use of trap-based positron beam sources to study collision processes with improved energy resolution. State-resolved measurements of electronic and vibrational excitation cross sections and measurement of annihilation rates in atoms and molecules as a function of incident positron energy are discussed. Where data are available, comparisons are made with analogous electron scattering cross sections. Resonance phenomena, common in electron scattering, appear to be less common in positron scattering. Possible exceptions include the sharp onsets of positron-impact electronic and vibrational excitation of selected molecules. Recent energy-resolved studies of positron annihilation in hydrocarbons containing more than a few carbon atoms provide direct evidence that vibrational Feshbach resonances underpin the anomalously large annihilation rates observed for many polyatomic species. We discuss open questions regarding this process in larger molecules, as well as positron annihilation in smaller molecules where the theoretical picture is less clear. (topical review)

  12. Electronic interaction between nitrogen-doped graphene and porphyrin molecules.

    Science.gov (United States)

    Pham, Van Dong; Lagoute, Jérôme; Mouhoub, Ouafi; Joucken, Frédéric; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie

    2014-09-23

    The chemical doping of graphene is a promising route to improve the performances of graphene-based devices through enhanced chemical reactivity, catalytic activity, or transport characteristics. Understanding the interaction of molecules with doped graphene at the atomic scale is therefore a leading challenge to be overcome for the development of graphene-based electronics and sensors. Here, we use scanning tunneling microscopy and spectroscopy to study the electronic interaction of pristine and nitrogen-doped graphene with self-assembled tetraphenylporphyrin molecules. We provide an extensive measurement of the electronic structure of single porphyrins on Au(111), thus revealing an electronic decoupling effect of the porphyrins adsorbed on graphene. A tip-induced switching of the inner hydrogen atoms of porphyrins, first identified on Au(111), is observed on graphene, allowing the identification of the molecular conformation of porphyrins in the self-assembled molecular layer. On nitrogen-doped graphene, a local modification of the charge transfer around the nitrogen sites is evidenced via a downshift of the energies of the molecular elecronic states. These data show how the presence of nitrogen atoms in the graphene network modifies the electronic interaction of organic molecules with graphene. These results provide a basic understanding for the exploitation of doped graphene in molecular sensors or nanoelectronics.

  13. Disordered Markovian Brownian ratchets.

    Science.gov (United States)

    Alicki, R

    1999-09-01

    A model of a Brownian ratchet coupled to a heat bath and driven by a nonequilibrium Poisson white noise is discussed. The formula describing a generated current in terms of the statistical properties of a possible irregular or random potential is derived within the small nonequilibrium noise approximation and illustrated by a few concrete examples. The perturbation technique for Hilbert space operators is used as a mathematical tool.

  14. Collision of hydrogen molecules interacting with two grapheme sheets

    Directory of Open Access Journals (Sweden)

    Malivuk-Gak Dragana

    2017-01-01

    Full Text Available It have been performed the computational experiments with two hydrogen molecules and two graphene sheets. Hydrogen - hydrogen and hydrogen - carbon interactions are described by Lennard - Jones potential. Equations of motion of the wave packet centre are solved numerically. The initial molecule velocity was determined by temperature and collisions occur in central point between two sheets. The molecules after collision stay near or get far away of graphene sheets. Then one can find what temperatures, graphene sheet sizes and their distances are favourable for hydrogen storage. It is found that quantum corrections of the molecule classical trajectories are not significant here. Those investigations of possibility of hydrogen storage by physisorption are of interest for improvement of the fuel cell systems. The main disadvantages of computational experiments are: (1 it cannot compute with very large number of C atoms, (2 it is assumed that carbon atoms are placed always in their equilibrium positions and (3 the changes of wave packet width are not considered.

  15. Rotational dependence of Fermi-type resonance interactions in molecules

    Science.gov (United States)

    Mikhailov, Vladimir M.; Smirnov, M. A.

    1997-03-01

    In Pasadena, (Milliken Lab., USA, 1930) F. Rossetti has observed in Raman spectrum of carbon-dioxide molecule the full symmetric vibration of carbon dioxide appeared as the group of four near lying lines instead of the waited single line. The true interpretation of this enigmatic effect (in that time) was given by E. Fermi -- accidental degeneration of the first excited state of the full symmetric vibration in carbon dioxide. It was the first example of the event observed later in various organic molecules. This event was named as resonance Fermi. The rotational dependence of Fermi type resonance interactions in quasirigid molecules in dominant approximation can be selected in an expansion of the effective vibration-rotation Hamiltonian Hvib- roteff by the operator H(g)(Fermi) equals H30 plus (Sigma) nH3n(g). Let us consider in detail the problem of the construction of the effective vibration-rotational Hamiltonian HVR yields Heff from the point of view of various ordering schemes (grouping) of the vibrational-rotational interactions with sequential analysis of the choice of the convenient grouping adequate to the spectroscopic problem.

  16. Constructive role of Brownian motion: Brownian motors and Stochastic Resonance

    Science.gov (United States)

    Hänggi, Peter

    2005-03-01

    Noise is usually thought of as the enemy of order rather as a constructive influence. For the phenomena of Stochastic Resonance [1] and Brownian motors [2], however, stochastic noise can play a beneficial role in enhancing detection and/or facilitating directed transmission of information in absence of biasing forces. Brownian motion assisted Stochastic Resonance finds useful applications in physical, technological, biological and biomedical contexts [1,3]. The basic principles that underpin Stochastic Resonance are elucidated and novel applications for nonlinear classical and quantum systems will be addressed. The presence of non-equilibrium disturbances enables to rectify Brownian motion so that quantum and classical objects can be directed around on a priori designed routes in biological and physical systems (Brownian motors). In doing so, the energy from the haphazard motion of (quantum) Brownian particles is extracted to perform useful work against an external load. This very concept together with first experimental realizations are discussed [2,4,5]. [1] L. Gammaitoni, P. Hä'nggi, P. Jung and F. Marchesoni, Stochastic Resonance, Rev. Mod. Phys. 70, 223 (1998).[2] R. D. Astumian and P. Hä'nggi, Brownian motors, Physics Today 55 (11), 33 (2002).[3] P. Hä'nggi, Stochastic Resonace in Physics and Biology, ChemPhysChem 3, 285 (2002).[4] H. Linke, editor, Special Issue on Brownian Motors, Applied Physics A 75, No. 2 (2002).[5] P. Hä'nggi, F. Marchesoni, F. Nori, Brownian motors, Ann. Physik (Leipzig) 14, xxx (2004); cond-mat/0410033.

  17. Coherent interaction of single molecules and plasmonic nanowires

    Science.gov (United States)

    Gerhardt, Ilja; Grotz, Bernhard; Siyushev, Petr; Wrachtrup, Jörg

    2017-09-01

    Quantum plasmonics opens the option to integrate complex quantum optical circuitry onto chip scale devices. In the past, often external light sources were used and nonclassical light was coupled in and out of plasmonic structures, such as hole arrays or waveguide structures. Another option to launch single plasmonic excitations is the coupling of single emitters in the direct proximity of, e.g., a silver or gold nanostructure. Here, we present our attempts to integrate the research of single emitters with wet-chemically grown silver nanowires. The emitters of choice are single organic dye molecules under cryogenic conditions, which are known to act as high-brightness and extremely narrow-band single photon sources. Another advantage is their high optical nonlinearity, such that they might mediate photon-photon interactions on the nanoscale. We report on the coupling of a single molecule fluorescence emission through the wire over the length of several wavelengths. The transmission of coherently emitted photons is proven by an extinction type experiment. As for influencing the spectral properties of a single emitter, we are able to show a remote change of the line-width of a single terrylene molecule, which is in close proximity to the nanowire.

  18. Spin interactions in Graphene-Single Molecule Magnets Hybrids

    Science.gov (United States)

    Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Aña; Luis, Fernando; Rauschenbach, Stephan; Dressel, Martin; Kern, Klaus; Burghard, Marko; Bogani, Lapo

    2014-03-01

    Graphene is a potential component of novel spintronics devices owing to its long spin diffusion length. Besides its use as spin-transport channel, graphene can be employed for the detection and manipulation of molecular spins. This requires an appropriate coupling between the sheets and the single molecular magnets (SMM). Here, we present a comprehensive characterization of graphene-Fe4 SMM hybrids. The Fe4 clusters are anchored non-covalently to the graphene following a diffusion-limited assembly and can reorganize into random networks when subjected to slightly elevated temperature. Molecules anchored on graphene sheets show unaltered static magnetic properties, whilst the quantum dynamics is profoundly modulated. Interaction with Dirac fermions becomes the dominant spin-relaxation channel, with observable effects produced by graphene phonons and reduced dipolar interactions. Coupling to graphene drives the spins over Villain's threshold, allowing the first observation of strongly-perturbative tunneling processes. Preliminary spin-transport experiments at low-temperature are further presented.

  19. Singlet-triplet interaction in linear triatomic molecules

    Science.gov (United States)

    Osherov, V. I.; Osherov, M. V.; Poluyanov, L. V.

    2018-01-01

    We present here two-electronic model, which describes singlet-triplet interaction 1 π -3Σ+ in linear triatomic molecules. The analysis takes into account spin-orbital coupling terms in electronic Hamiltonian, as well as its symmetry properties. We give the symmetry operators of electronic Hamiltonian including space operators (acting on electronic coordinates) and matrix operators (acting on electronic spin). We consider only deformation π -modes and our resulting 5 × 5 vibronic matrix describes actual relativistic pseudo-Renner effect (1 π -3 Σ) × π . The eigenvalues of vibronic matrix (i.e. potential energy surfaces) have axial symmetry and represented by analytical expressions, include five electrostatic and three spin-orbital parameters.

  20. A study on interaction of DNA molecules and carbon nanotubes for an effective ejection of the molecules

    International Nuclear Information System (INIS)

    Wu, N.; Wang, Q.

    2012-01-01

    The ejection of DNA molecules from carbon nanotubes is reported from interaction energy perspectives by molecular dynamics simulations. The critical ejection energy, which is to be applied to a DNA molecule for a successful ejection from a carbon nanotube, is investigated based on a study on the friction and binding energy between the DNA molecule and the tube. An effective ejection is realized by subjecting a kinetic energy on the DNA molecule that is larger than the solved critical ejection energy. In addition, the relationship between ejection energies and sizes of DNA molecules and carbon nanotubes is investigated. -- Highlights: ► Report the ejection of DNA molecules from CNTs from interaction energy perspectives. ► Develop a methodology for the critical energy of an effective ejection of a DNA molecule from a CNT. ► Present the relationship between critical ejection energies and sizes of DNA molecules and CNTs. ► Provide a general guidance on the ejection of encapsulated molecules from CNTs.

  1. Fundamental properties of molecules on surfaces. Molecular switching and interaction of magnetic molecules with superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hatter, Nino

    2016-12-14

    In this thesis, we investigate individual molecular switches and metal-organic complexes on surfaces with scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperatures. One focus addresses the switching ability and mechanism of diarylethene on Ag(111). The other focus lies on resolving and tuning magnetic interactions of individual molecules with superconductors. 4,4'-(4,4'-(perfluorocyclopent-1-ene-1,2-diyl)bis (5-methylthiophene-4,2-diyl)dip yridine (PDTE) is a prototypical photochromic switch. We can induce a structural change of individual PDTE molecules on Ag(111) with the STM tip. This change is accompanied by a reduction of the energy gap between the occupied and unoccupied molecular orbitals. Density functional theory (DFT) calculations reveal that the induced switching corresponds to a ring-closing reaction from an open isomer in a flat adsorption configuration to a ring-closed isomer with its methyl groups in a cis configuration. The final product is thermodynamically stabilized by strong dispersion interactions with the surface. A linear dependence of the switching threshold with the tip-sample distance with a minimal threshold of 1.4 V is found, which we assign to a combination of an electric-field induced process and a tunneling-electron contribution. DFT calculations suggest a large activation barrier for a ring-closing reaction from the open flat configuration into the closed cis configuration. The interaction of magnetic molecules with superconductors is studied on manganese phthalocyanine (MnPc) adsorbed on Pb(111). We find triplets of Shiba states inside the superconducting gap. Different adsorption sites of MnPc provide a large variety of exchange coupling strengths, which lead to a collective energy shift of the Shiba triplets. We can assign the splitting of the Shiba states to be an effect of magnetic anisotropy in the system. A quantum phase transition from a ''Kondo screened'' to a &apos

  2. How superdiffusion gets arrested: ecological encounters explain shift from Lévy to Brownian movement.

    Science.gov (United States)

    de Jager, Monique; Bartumeus, Frederic; Kölzsch, Andrea; Weissing, Franz J; Hengeveld, Geerten M; Nolet, Bart A; Herman, Peter M J; van de Koppel, Johan

    2014-01-07

    Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when foraging in resource-poor environments. Yet, empirical studies reveal animals moving in a Brownian fashion when resources are abundant. We demonstrate that Einstein's original theory of collision-induced Brownian motion in physics provides a parsimonious, mechanistic explanation for these observations. Here, Brownian motion results from frequent encounters between organisms in dense environments. In density-controlled experiments, movement patterns of mussels shifted from Lévy towards Brownian motion with increasing density. When the analysis was restricted to moves not truncated by encounters, this shift did not occur. Using a theoretical argument, we explain that any movement pattern approximates Brownian motion at high-resource densities, provided that movement is interrupted upon encounters. Hence, the observed shift to Brownian motion does not indicate a density-dependent change in movement strategy but rather results from frequent collisions. Our results emphasize the need for a more mechanistic use of Brownian motion in ecology, highlighting that especially in rich environments, Brownian motion emerges from ecological interactions, rather than being a default movement pattern.

  3. Archimedes' principle for Brownian liquid

    OpenAIRE

    Burdzy, Krzysztof; Chen, Zhen-Qing; 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 ...

  4. q-deformed Brownian motion

    CERN Document Server

    Man'ko, V I

    1993-01-01

    Brownian motion may be embedded in the Fock space of bosonic free field in one dimension.Extending this correspondence to a family of creation and annihilation operators satisfying a q-deformed algebra, the notion of q-deformation is carried from the algebra to the domain of stochastic processes.The properties of q-deformed Brownian motion, in particular its non-Gaussian nature and cumulant structure,are established.

  5. Neural cell adhesion molecule differentially interacts with isoforms of the fibroblast growth factor receptor

    DEFF Research Database (Denmark)

    Christensen, Claus; Berezin, Vladimir; Bock, Elisabeth

    2011-01-01

    The fibroblast growth factor receptor (FGFR) can be activated through direct interactions with various fibroblast growth factors or through a number of cell adhesion molecules, including the neural cell adhesion molecule (NCAM). We produced recombinant proteins comprising the ligand...

  6. Efficient reactive Brownian dynamics

    Science.gov (United States)

    Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

    2018-01-01

    We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which

  7. Positron interactions and transport in biologically relevant molecules

    International Nuclear Information System (INIS)

    Makochekanwa, C; Jones, A; Caradonna, P; Slaughter, D; Sullivan, J; Buckman, S; Bankovic, A; Petrovic, Z; Malovic, G; Dujko, S; Marler, J; Nixon, K; Brunger, M

    2009-01-01

    We present new, high-resolution measurements of positron scattering from biologically relevant molecules, such as water and formic acid. The measurements include absolute determinations of total scattering and positronium formation and they have enabled us to assemble a set of cross sections for these molecules which can be used in an investigation of positron transport in these systems.

  8. Limits of bifractional Brownian noises

    OpenAIRE

    Maejima, Makoto; Tudor, Ciprian

    2008-01-01

    International audience; Let $B^{H,K}=\\left (B^{H,K}_{t}, t\\geq 0\\right )$ be a bifractional Brownian motion with two parameters $H\\in (0,1)$ and $K\\in(0,1]$. The main result of this paper is that the increment process generated by the bifractional Brownian motion $\\left( B^{H,K}_{h+t} -B^{H,K} _{h}, t\\geq 0\\right)$ converges when $h\\to \\infty$ to $\\left (2^{(1-K)/{2}}B^{HK} _{t}, t\\geq 0\\right )$, where $\\left (B^{HK}_{t}, t\\geq 0\\right)$ is the fractional Brownian motion with Hurst index $HK...

  9. Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways

    Science.gov (United States)

    Li, Yan; Li, Weiguo; Chen, Xin; Sun, Jiatong; Chen, Huan; Lv, Sali

    2014-01-01

    Previous studies have indicated that the downstream proteins in a key pathway can be potential drug targets and that the pathway can play an important role in the action of drugs. So pathways could be considered as targets of small molecules. A link map between small molecules and pathways was constructed using gene expression profile, pathways, and gene expression of cancer cell line intervened by small molecules and then we analysed the topological characteristics of the link map. Three link patterns were identified based on different drug discovery implications for breast, liver, and lung cancer. Furthermore, molecules that significantly targeted the same pathways tended to treat the same diseases. These results can provide a valuable reference for identifying drug candidates and targets in molecularly targeted therapy. PMID:25114931

  10. Rotation-vibrational spectra of diatomic molecules and nuclei with Davidson interactions

    CERN Document Server

    Rowe, D J

    1998-01-01

    Complete rotation-vibrational spectra and electromagnetic transition rates are obtained for Hamiltonians of diatomic molecules and nuclei with Davidson interactions. Analytical results are derived by dynamical symmetry methods for diatomic molecules and a liquid-drop model of the nucleus. Numerical solutions are obtained for a many-particle nucleus with quadrupole Davidson interactions within the framework of the microscopic symplectic model. (author)

  11. Dispersion interaction between an atom and linear molecule

    International Nuclear Information System (INIS)

    Carvalho, I.L. de

    1987-01-01

    The Jacobi-Csanak method is adapted to the calculation of the dipole-dipole, dipole-quadrupole, quadrupole-dipole, and quadrupole-quadrupole terms of the dispersion energy of an atom-linear molecule system. The angle-dependent parts of the Born amplitudes for the linear molecule are represented by real spherical harmonics. The dispersion energy is finite at all distances and reproduces the usual expression in the asymptotic region (R≥4.7 (angstrom)). In the intermediary region (2.4(angstrom) ≤ R [pt

  12. Brownian motion of solitons in a Bose-Einstein condensate.

    Science.gov (United States)

    Aycock, Lauren M; Hurst, Hilary M; Efimkin, Dmitry K; Genkina, Dina; Lu, Hsin-I; Galitski, Victor M; Spielman, I B

    2017-03-07

    We observed and controlled the Brownian motion of solitons. We launched solitonic excitations in highly elongated [Formula: see text] Bose-Einstein condensates (BECs) and showed that a dilute background of impurity atoms in a different internal state dramatically affects the soliton. With no impurities and in one dimension (1D), these solitons would have an infinite lifetime, a consequence of integrability. In our experiment, the added impurities scatter off the much larger soliton, contributing to its Brownian motion and decreasing its lifetime. We describe the soliton's diffusive behavior using a quasi-1D scattering theory of impurity atoms interacting with a soliton, giving diffusion coefficients consistent with experiment.

  13. Kinetic Energy of a Free Quantum Brownian Particle

    Directory of Open Access Journals (Sweden)

    Paweł Bialas

    2018-02-01

    Full Text Available We consider a paradigmatic model of a quantum Brownian particle coupled to a thermostat consisting of harmonic oscillators. In the framework of a generalized Langevin equation, the memory (damping kernel is assumed to be in the form of exponentially-decaying oscillations. We discuss a quantum counterpart of the equipartition energy theorem for a free Brownian particle in a thermal equilibrium state. We conclude that the average kinetic energy of the Brownian particle is equal to thermally-averaged kinetic energy per one degree of freedom of oscillators of the environment, additionally averaged over all possible oscillators’ frequencies distributed according to some probability density in which details of the particle-environment interaction are present via the parameters of the damping kernel.

  14. Studying small molecule-aptamer interactions using MicroScale Thermophoresis (MST).

    Science.gov (United States)

    Entzian, Clemens; Schubert, Thomas

    2016-03-15

    Aptamers are potent and versatile binding molecules recognizing various classes of target molecules. Even challenging targets such as small molecules can be identified and bound by aptamers. Studying the interaction between aptamers and drugs, antibiotics or metabolites in detail is however difficult due to the lack of sophisticated analysis methods. Basic binding parameters of these small molecule-aptamer interactions such as binding affinity, stoichiometry and thermodynamics are elaborately to access using the state of the art technologies. The innovative MicroScale Thermophoresis (MST) is a novel, rapid and precise method to characterize these small molecule-aptamer interactions in solution at microliter scale. The technology is based on the movement of molecules through temperature gradients, a physical effect referred to as thermophoresis. The thermophoretic movement of a molecule depends - besides on its size - on charge and hydration shell. Upon the interaction of a small molecule and an aptamer, at least one of these parameters is altered, leading to a change in the movement behavior, which can be used to quantify molecular interactions independent of the size of the target molecule. The MST offers free choice of buffers, even measurements in complex bioliquids are possible. The dynamic affinity range covers the pM to mM range and is therefore perfectly suited to analyze small molecule-aptamer interactions. This section describes a protocol how quantitative binding parameters for aptamer-small molecule interactions can be obtained by MST. This is demonstrated by mapping down the binding site of the well-known ATP aptamer DH25.42 to a specific region at the adenine of the ATP molecule. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Quantum equations from Brownian motions

    International Nuclear Information System (INIS)

    Rajput, B.S.

    2011-01-01

    Classical Schrodinger and Dirac equations have been derived from Brownian motions of a particle, it has been shown that the classical Schrodinger equation can be transformed to usual Schrodinger Quantum equation on applying Heisenberg uncertainty principle between position and momentum while Dirac Quantum equation follows it's classical counter part on applying Heisenberg uncertainly principle between energy and time without applying any analytical continuation. (author)

  16. Interacting Dark Resonances with Plasmonic Meta-Molecules

    Science.gov (United States)

    2014-09-17

    full electrodynamics simulations to corroborate our results. Such multilayered meta-molecules can bring a new dimension to higher quality factor...exhibit many remarkable phenomena in atom optics,1 cavity quan- tum electrodynamics (cQED),2 quantum computation, and quantum information.3 For instance...Several classical or plasmonic analogue of quantum optical phenom- ena like plasmon induced transparency (PIT),5,6 electromag- netic induced

  17. Examining small molecule: HIV RNA interactions using arrayed imaging reflectometry

    Science.gov (United States)

    Chaimayo, Wanaruk; Miller, Benjamin L.

    2014-03-01

    Human Immunodeficiency Virus (HIV) has been the subject of intense research for more than three decades as it causes an uncurable disease: Acquired Immunodeficiency Syndrome, AIDS. In the pursuit of a medical treatment, RNAtargeted small molecules are emerging as promising targets. In order to understand the binding kinetics of small molecules and HIV RNA, association (ka) and dissociation (kd) kinetic constants must be obtained, ideally for a large number of sequences to assess selectivity. We have developed Aqueous Array Imaged Reflectometry (Aq-AIR) to address this challenge. Using a simple light interference phenomenon, Aq-AIR provides real-time high-throughput multiplex capabilities to detect binding of targets to surface-immobilized probes in a label-free microarray format. The second generation of Aq-AIR consisting of high-sensitivity CCD camera and 12-μL flow cell was fabricated. The system performance was assessed by real-time detection of MBNL1-(CUG)10 and neomycin B - HIV RNA bindings. The results establish this second-generation Aq-AIR to be able to examine small molecules binding to RNA sequences specific to HIV.

  18. Interaction of ultrashort pulses with molecules and solids: Physics

    Indian Academy of Sciences (India)

    2014-07-26

    Jul 26, 2014 ... The physics of interaction has been fairly understood over the last couple of decades and, consequently, several applications have been envisaged from these interactions in the fields of photonics, lithography, biomedicine, sensing, telecommunications etc. In the present article we describe three different ...

  19. Interaction between a "processed" ovalbumin peptide and Ia molecules

    DEFF Research Database (Denmark)

    Buus, S; Colon, S; Smith, C

    1986-01-01

    -339)-Tyr. As a further specificity control, we also used the chicken egg lysozyme peptide Tyr-(46-61), which has recently been studied by similar methods [Babbitt, B. P., Allen, P. M., Matsueda, G., Haber, E. & Unanue, E. R. (1985) Nature (London) 317, 359-361]. We have confirmed that it bound to I......The binding of 125I-labeled immunogenic peptides to purified Ia molecules in detergent solution was examined by equilibrium dialysis. We used the chicken ovalbumin peptide ovalbumin-(323-339)-Tyr, which is immunogenic in the BALB/c mouse and restricted to I-Ad. 125I-labeled ovalbumin-(323-339)-Tyr...

  20. Interaction between perylene-derivated molecules observed by low temperature scanning tunneling microscopy

    Science.gov (United States)

    Vernisse, Loranne; Guillermet, Olivier; Gourdon, André; Coratger, Roland

    2018-03-01

    Derivative perylene molecules deposited on Ag(111) and on NaCl(001) ultrathin layers have been investigated using low temperature STM and NC-AFM. When the metallic substrate is held at ambient temperature during evaporation, the molecules form characteristic trimers on the Ag(111) surface and interact through their polar groups. Close to the steps, the molecules form linear structures and seems to stand side by side. On the other hand, after deposition on a substrate cooled at liquid helium temperature, single molecules are observed both on metal and on NaCl. On the ultrathin insulator layers, the STM images present characteristic contrasts related to the molecular orbitals which favors the localization of aldehyde groups. In this case, the lateral molecular interactions may induce the formation of small assemblies in which the electronic levels are slightly shifted. A possible interpretation of this phenomenon is to take into account polar interactions and charge transfer between neighboring molecules.

  1. Synthetic models related to DNA-intercalating molecules. Interactions between 8-alkoxypsoralen and adenine

    International Nuclear Information System (INIS)

    Decout, J.L.; Lhomme, J.

    1983-01-01

    To investigate the interactions and the photoreactions between furocoumarins and adenine, compounds in which a psoralen molecule is linked by different polymethylene bridges have been synthesised. Ring-ring intramolecular interactions are observed by UV spectroscopy. Thermodynamic parameters of these hydrophobic interactions are determined by the study of the variation of the hypochromic effect with temperature. (author)

  2. Ratcheted electrophoresis of Brownian particles

    Energy Technology Data Exchange (ETDEWEB)

    Kowalik, Mikołaj; Bishop, Kyle J. M., E-mail: kjmbishop@engr.psu.edu [Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2016-05-16

    The realization of nanoscale machines requires efficient methods by which to rectify unbiased perturbations to perform useful functions in the presence of significant thermal noise. The performance of such Brownian motors often depends sensitively on their operating conditions—in particular, on the relative rates of diffusive and deterministic motions. In this letter, we present a type of Brownian motor that uses contact charge electrophoresis of a colloidal particle within a ratcheted channel to achieve directed transport or perform useful work against an applied load. We analyze the stochastic dynamics of this model ratchet to show that it functions under any operating condition—even in the limit of strong thermal noise and in contrast to existing ratchets. The theoretical results presented here suggest that ratcheted electrophoresis could provide a basis for electrochemically powered, nanoscale machines capable of transport and actuation of nanoscale components.

  3. Structural requirements for the interaction between peptide antigens and I-Ed molecules

    DEFF Research Database (Denmark)

    Sette, A; Adorini, L; Appella, E

    1989-01-01

    We have analyzed the structural characteristics of the interaction between I-Ed molecules and their peptide ligands. It was found that unrelated good I-Ed binders share structurally similar "core" regions that were experimentally demonstrated to be crucial for binding to I-Ed molecules. Single am...

  4. p-adic Brownian motion

    Science.gov (United States)

    Zelenov, E. I.

    2016-12-01

    We define p-adic Brownian motion (Wiener process) and study its properties. We construct a presentation of the trajectories of this process by their series expansions with respect to van der Put's basis and show that they are nowhere differentiable functions satisfying the p-adic Lipschitz condition of order 1. We define the p-adic Wiener measure on the space of continuous functions and study its properties.

  5. Extremes of multifractional Brownian motion

    OpenAIRE

    Bai, Long

    2017-01-01

    Let $B_{H}(t), t\\geq [0,T], T\\in(0,\\infty)$ be the standard Multifractional Brownian Motion(mBm), in this contribution we are concerned with the exact asymptotics of \\begin{eqnarray*} \\mathbb{P}\\left\\{\\sup_{t\\in[0,T]}B_{H}(t)>u\\right\\} \\end{eqnarray*} as $u\\rightarrow\\infty$. Mainly depended on the structures of $H(t)$, the results under several important cases are investigated.

  6. 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.

  7. 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.

  8. Flicker Noise as a Probe of Electronic Interaction at Metal-Single Molecule Interfaces.

    Science.gov (United States)

    Adak, Olgun; Rosenthal, Ethan; Meisner, Jeffery; Andrade, Erick F; Pasupathy, Abhay N; Nuckolls, Colin; Hybertsen, Mark S; Venkataraman, Latha

    2015-06-10

    Charge transport properties of metal-molecule interfaces depend strongly on the character of molecule-electrode interactions. Although through-bond coupled systems have attracted the most attention, through-space coupling is important in molecular systems when, for example, through-bond coupling is suppressed due to quantum interference effects. To date, a probe that clearly distinguishes these two types of coupling has not yet been demonstrated. Here, we investigate the origin of flicker noise in single molecule junctions and demonstrate how the character of the molecule-electrode coupling influences the flicker noise behavior of single molecule junctions. Importantly, we find that flicker noise shows a power law dependence on conductance in all junctions studied with an exponent that can distinguish through-space and through-bond coupling. Our results provide a new and powerful tool for probing and understanding coupling at the metal-molecule interface.

  9. Molecular simulation of polar molecules interaction with MOFs family materials

    International Nuclear Information System (INIS)

    De Toni, M.

    2012-01-01

    The topic of this thesis is the adsorption of simple molecular fluids in nano-porous materials. Many industrial processes are based on this phenomenon, including ionic exchange, selective separation and heterogeneous catalysis. I used molecular simulation to study the adsorption properties of polar molecules of industrial interest (CO 2 and H 2 O) in a new class of crystalline microporous hybrid organic-inorganic materials called Metal-Organic Frameworks (MOFs). They have exceptional adsorption properties due to their topological variety and their versatility, allowed by the large range of possibilities offered by organic and coordination chemistry and functionalizations. I first studied the adsorption of CO 2 in a family of materials called IRMOFs, which share the same topology but have different porous volume, in order to characterize the effect of confinement on their adsorption performance. In particular, a general behavior has been highlighted: the critical temperature decreases when the confinement increases. Then, I looked at a recently synthesized cationic MOF called Zn2(CBTACN). After having localized the extra-framework halogen anions in the unit cell of the material, something which was not possible experimentally, I characterized CO 2 adsorption in this system first as a pure gas and then as a component of different mixtures. Finally, I was interested in the hydrothermal stability of MOFs, a crucial issue for their use in industrial applications. I observed the hydration mechanism of system that is analogous to the MOF-5 (IRMOF-0h) and shed light on some collaborative effects of the attack of water that were unknown to in the literature. (author)

  10. Flavonoids as Important Molecules of Plant Interactions with the Environment

    Directory of Open Access Journals (Sweden)

    Justyna Mierziak

    2014-10-01

    Full Text Available Flavonoids are small molecular secondary metabolites synthesized by plants with various biological activities. Due to their physical and biochemical properties, they are capable of participating in plants’ interactions with other organisms (microorganisms, animals and other plants and their reactions to environmental stresses. The majority of their functions result from their strong antioxidative properties. Although an increasing number of studies focus on the application of flavonoids in medicine or the food industry, their relevance for the plants themselves also deserves extensive investigations. This review summarizes the current knowledge on the functions of flavonoids in the physiology of plants and their relations with the environment.

  11. Computational probing protein-protein interactions targeting small molecules.

    Science.gov (United States)

    Wang, Yong-Cui; Chen, Shi-Long; Deng, Nai-Yang; Wang, Yong

    2016-01-15

    With the booming of interactome studies, a lot of interactions can be measured in a high throughput way and large scale datasets are available. It is becoming apparent that many different types of interactions can be potential drug targets. Compared with inhibition of a single protein, inhibition of protein-protein interaction (PPI) is promising to improve the specificity with fewer adverse side-effects. Also it greatly broadens the drug target search space, which makes the drug target discovery difficult. Computational methods are highly desired to efficiently provide candidates for further experiments and hold the promise to greatly accelerate the discovery of novel drug targets. Here, we propose a machine learning method to predict PPI targets in a genomic-wide scale. Specifically, we develop a computational method, named as PrePPItar, to Predict PPIs as drug targets by uncovering the potential associations between drugs and PPIs. First, we survey the databases and manually construct a gold-standard positive dataset for drug and PPI interactions. This effort leads to a dataset with 227 associations among 63 PPIs and 113 FDA-approved drugs and allows us to build models to learn the association rules from the data. Second, we characterize drugs by profiling in chemical structure, drug ATC-code annotation, and side-effect space and represent PPI similarity by a symmetrical S-kernel based on protein amino acid sequence. Then the drugs and PPIs are correlated by Kronecker product kernel. Finally, a support vector machine (SVM), is trained to predict novel associations between drugs and PPIs. We validate our PrePPItar method on the well-established gold-standard dataset by cross-validation. We find that all chemical structure, drug ATC-code, and side-effect information are predictive for PPI target. Moreover, we can increase the PPI target prediction coverage by integrating multiple data sources. Follow-up database search and pathway analysis indicate that our new

  12. The Diffusion Process in Small Particles and Brownian Motion

    Science.gov (United States)

    Khoshnevisan, M.

    Albert Einstein in 1926 published his book entitled ''INVESTIGATIONS ON THE THEORY OF THE BROWNIAN MOVEMENT''. He investigated the process of diffusion in an undissociated dilute solution. The diffusion process is subject to Brownian motion. Furthermore, he elucidated the fact that the heat content of a substance will change the position of the single molecules in an irregular fashion. In this paper, I have shown that in order for the displacement of the single molecules to be proportional to the square root of the time, and for v/2 - v 1 Δ =dv/dx , (where v1 and v2 are the concentrations in two cross sections that are separated by a very small distance), ∫ - ∞ ∞ Φ (Δ) dΔ = I and I/τ ∫ - ∞ ∞Δ2/2 Φ (Δ) dΔ = D conditions to hold, then equation (7a) D =√{ 2 D }√{ τ} must be changed to Δ =√{ 2 D }√{ τ} . I have concluded that D =√{ 2 D }√{ τ} is an unintended error, and it has not been amended for almost 90 years in INVESTIGATIONS ON THE THEORY OF THE BROWNIAN MOVEMENT, 1926 publication.

  13. Thermodynamic and Quantum Thermodynamic Analyses of Brownian Movement

    OpenAIRE

    Gyftopoulos, Elias P.

    2006-01-01

    Thermodynamic and quantum thermodynamic analyses of Brownian movement of a solvent and a colloid passing through neutral thermodynamic equilibrium states only. It is shown that Brownian motors and E. coli do not represent Brownian movement.

  14. Interaction of a single acetophenone molecule with group III-IV elements mediated by Si(001)

    Science.gov (United States)

    Racis, A.; Jurczyszyn, L.; Radny, M. W.

    2018-03-01

    A theoretical study of an influence of the acetophenone molecule adsorbed on the Si(001) on the local chemical reactivity of silicon surface is presented. The obtained results indicate that the interaction of the molecule with silicon substrate breaks the intra-dimer π bonds in four surface silicon dimers interacting directly with adsorbed molecule. This leads to the formation of two pairs of unpaired dangling bonds at two opposite sides of the molecule. It is demonstrated that these dangling bonds increase considerably the local chemical reactivity of the silicon substrate in the vicinity of the adsorbed molecule. Consequently, it is shown that such molecule bonded with Si(001) can stabilize the position of In and Pb adatoms diffusing on silicon substrate at two sides and initiate the one-dimensional aggregation of the metallic adatoms on the Si(001) substrate anchored at both sides of the adsorbed molecule. This type of aggregation leads to the growth of chain-like atomic structures in opposite directions, pinned to adsorbed molecule and oriented perpendicular to the rows of surface silicon dimers.

  15. Engineering Autonomous Chemomechanical Nanomachines Using Brownian Ratchets

    Science.gov (United States)

    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

  16. Structural requirements for the interaction between class II MHC molecules and peptide antigens

    DEFF Research Database (Denmark)

    Sette, A; Buus, S; Appella, E

    1990-01-01

    IA(d) and IE(d) molecules and their peptide ligands, we found that some structural characteristics apply to both antigen-MHC interactions. In particular, we found: 1) each MHC molecule is capable of binding many unrelated peptides through the same peptide-binding site; 2) despite this permissiveness......Previous work from our and other laboratories indicates that T cells recognize a complex between the MHC restriction element and peptide antigen fragments. This paper reviews the structural characteristics of the formation of such a complex. By analyzing in detail the interactions between purified...... of binding, it is possible to define certain structural features of peptides that are associated with the capacity to bind to a particular MHC specificity (IA(d) or IE(d)); 3) IA(d) and IE(d) molecules recognize different and independent structures on the antigen molecule; 4) only about 10% of the single...

  17. Interactions Between Charged Macroions Mediated by Molecules with Rod-like Charged Structures

    Directory of Open Access Journals (Sweden)

    Bohinc, K.

    2014-03-01

    Full Text Available A short review of recent theoretical advances in studies of the interaction between highly charged systems embedded in a solution of rod-like molecules is presented. The system is theoretically described by the functional density theory, where the correlations within the rod-like molecules are accounted for. We show that for sufficiently long molecules and large surface charge densities, an attractive force between like-charged surfaces arises due to the spatially distributed charges within the molecules. The added salt has an influence on the condition for the attractive force between like-charged surfaces. The theoretical results are compared with Monte Carlo simulations. Many phenomena motivate the study of the interaction between like-charged surfaces (DNA condensation, virus aggregation, yeast flocculation, cohesion of cement paste.

  18. Relativistic Brownian motion: From a microscopic binary collision model to the Langevin equation

    OpenAIRE

    Dunkel, Jörn; Hänggi, Peter (Prof. Dr. Dr. h.c. mult.)

    2006-01-01

    The Langevin equation (LE) for the one-dimensional relativistic Brownian motion is derived from a microscopic collision model. The model assumes that a heavy point-like Brownian particle interacts with the lighter heat bath particles via elastic hard-core collisions. First, the commonly known, non-relativistic LE is deduced from this model, by taking into account the non-relativistic conservation laws for momentum and kinetic energy. Subsequently, this procedure is generalized to the relativi...

  19. Effect of ligand substitution on the exchange interactions in {Mn12}-type single-molecule magnets

    OpenAIRE

    Boukhvalov, D. W.; Dobrovitski, V. V.; Kögerler, P.; Al-Saqer, M.; Katsnelson, M. I.; Lichtenstein, A. I.; Harmon, B. N.

    2010-01-01

    We investigate how the ligand substitution affects the intra-molecular spin exchange interactions, studying a prototypal family of single-molecule magnets comprising dodecanuclear cluster molecules [Mn12O12(COOR)16]. We identify a simple scheme based on accumulated Pauling electronegativity numbers (a.e.n.) of the carboxylate ligand groups (R). The redistribution of the electron density, controlled by a.e.n. of a ligand, changes the degree of hybridization between 3d electrons of manganese an...

  20. First Principles Study on the Interaction Mechanisms of Water Molecules on TiO2 Nanotubes

    Directory of Open Access Journals (Sweden)

    Jianhong Dai

    2016-12-01

    Full Text Available The adsorption properties of water molecules on TiO2 nanotubes (TiO2NT and the interaction mechanisms between water molecules are studied by first principles calculations. The adsorption preferences of water molecules in molecular or dissociated states on clean and H-terminated TiO2NT are evaluated. Adsorption of OH clusters on (0, 6 and (9, 0 TiO2 nanotubes are first studied. The smallest adsorption energies are −1.163 eV and −1.383 eV, respectively, by examining five different adsorption sites on each type of tube. Eight and six adsorption sites were considered for OH adsorbtion on the H terminated (0, 6 and (9, 0 nanotubes. Water molecules are reformed with the smallest adsorption energy of −4.796 eV on the former and of −5.013 eV on the latter nanotube, respectively. For the adsorption of a single water molecule on TiO2NT, the molecular state shows the strongest adsorption preference with an adsorption energy of −0.660 eV. The adsorption of multiple (two and three water molecules on TiO2NT is also studied. The calculated results show that the interactions between water molecules greatly affect their adsorption properties. Competition occurs between the molecular and dissociated states. The electronic structures are calculated to clarify the interaction mechanisms between water molecules and TiO2NT. The bonding interactions between H from water and oxygen from TiO2NT may be the reason for the dissociation of water on TiO2NT.

  1. Interaction of VUV-photons with molecules. Spectroscopy and dynamics of molecular superexcited states

    International Nuclear Information System (INIS)

    Hatano, Y.

    2002-01-01

    Complete text of publication follows. A survey is given of recent progress in experimental studies of the interaction of VUV-photons with molecules, i.e., those of photoabsorption, photoionization, and photodissociation of molecules in the excitation photon energy range of 10-50 eV, with a particular emphasis placed on current understanding of the spectroscopy and dynamics of formed molecular superexcited states. These studies are of great importance in understanding the interaction of ionizing radiation with matter. Molecules studied are ranged from simple diatomic and triatomic molecules to polyatomic molecules such as hydrocarbons. Most of the observed molecular superexcited states are assigned to high Rydber states which are vibrationally, doubly, or inner-core excited and converge to each of ion states. Non-Rydberg superexcited states are also observed. Dissociation into neutral fragments in comparison with ionization is of unexpectedly great importance in the observed decay of each of these state-assigned superexcited molecules. Dissociation dynamics as well as its products of superexcited states are remarkably different from those of lower excited states below about ionization thresholds. Some remarks are also presented of molecules in the condensed phase

  2. Interactions between nitrogen molecules and barium atoms on Ru (0001) surface

    International Nuclear Information System (INIS)

    Zhao Xinxin; Mi Yiming; Xu Hongxia; Wang Lili; Ren Li; Tao Xiangming; Tan Mingqiu

    2011-01-01

    We had performed first principles calculations on interactions between nitrogen molecules and barium atoms on Ru (0001) surface using density function theory methods. It was shown that effects of barium atoms weakened the bond strength of nitrogen molecules. The bond length of nitrogen molecule increases from 0.113 nm on Ru (001)-N 2 to 0.120 nm on Ru (001)-N 2 /Ba surface. While stretch vibrational frequency of nitrogen molecule decreased from 2222 cm -1 and charge transfer toward nitrogen molecule increased from 0.3 e to 1.1 e. Charge was mainly translated from 6 s orbitals of barium atoms to 4 d orbitals of substrate, which enhanced the hybridization between 4 d and 2 π orbitals and increased the dipole moment of 5 σ and d π orbitals of nitrogen molecule. The molecular dipole moment of nitrogen molecule was increased by -0.136 e Anstrom. It was suggested that barium had some characters to be an electronic promoter on the process of activating nitrogen molecules on Ru (0001) surface. (authors)

  3. Theory of molecule metal nano-particle interaction: Quantum description of plasmonic lasing

    International Nuclear Information System (INIS)

    Zhang, Yuan; May, Volkhard

    2015-01-01

    The recent quantum description of a few molecules interacting with plasmon excitations of a spherical metal nano-particle (MNP) as presented in the work of Zhang and May [Phys. Rev. B 89, 245441 (2014)] is extended to systems with up to 100 molecules. We demonstrate the possibility of multiple plasmon excitation and describe their conversion into far-field photons. The calculation of the steady-state photon emission spectrum results in an emission line-narrowing with an increasing number of molecules coupled to the MNP. This is considered as an essential criterion for the action of the molecule-MNP system as a nano-laser. To have exact results for systems with up to 20 molecules, we proceed as recently described by Richter et al. [Phys. Rev. B 91, 035306 (2015)] and study a highly symmetric system. It assumes an equatorial and regular position of identical molecules in such a way that their coupling is dominated by that to a single MNP dipole-plasmon excitation. Changing from the exact computation of the system’s complete density matrix to an approximate theory based on the reduced plasmon density matrix, systems with more than 100 molecules can be described. Finally, nonlinear rate equations are proposed which reproduce the mean number of excited plasmons in their dependence of the number of molecules and of the used pump rate. The second order intensity correlation function of emitted photons is related to the respective plasmon correlation function which approaches unity when the system starts lasing

  4. Collective motion of active Brownian particles with polar alignment.

    Science.gov (United States)

    Martín-Gómez, Aitor; Levis, Demian; Díaz-Guilera, Albert; Pagonabarraga, Ignacio

    2018-04-04

    We present a comprehensive computational study of the collective behavior emerging from the competition between self-propulsion, excluded volume interactions and velocity-alignment in a two-dimensional model of active particles. We consider an extension of the active brownian particles model where the self-propulsion direction of the particles aligns with the one of their neighbors. We analyze the onset of collective motion (flocking) in a low-density regime (10% surface area) and show that it is mainly controlled by the strength of velocity-alignment interactions: the competition between self-propulsion and crowding effects plays a minor role in the emergence of flocking. However, above the flocking threshold, the system presents a richer pattern formation scenario than analogous models without alignment interactions (active brownian particles) or excluded volume effects (Vicsek-like models). Depending on the parameter regime, the structure of the system is characterized by either a broad distribution of finite-sized polar clusters or the presence of an amorphous, highly fluctuating, large-scale traveling structure which can take a lane-like or band-like form (and usually a hybrid structure which is halfway in between both). We establish a phase diagram that summarizes collective behavior of polar active brownian particles and propose a generic mechanism to describe the complexity of the large-scale structures observed in systems of repulsive self-propelled particles.

  5. Efficient Isothermal Titration Calorimetry Technique Identifies Direct Interaction of Small Molecule Inhibitors with the Target Protein.

    Science.gov (United States)

    Gal, Maayan; Bloch, Itai; Shechter, Nelia; Romanenko, Olga; Shir, Ofer M

    2016-01-01

    Protein-protein interactions (PPI) play a critical role in regulating many cellular processes. Finding novel PPI inhibitors that interfere with specific binding of two proteins is considered a great challenge, mainly due to the complexity involved in characterizing multi-molecular systems and limited understanding of the physical principles governing PPIs. Here we show that the combination of virtual screening techniques, which are capable of filtering a large library of potential small molecule inhibitors, and a unique secondary screening by isothermal titration calorimetry, a label-free method capable of observing direct interactions, is an efficient tool for finding such an inhibitor. In this study we applied this strategy in a search for a small molecule capable of interfering with the interaction of the tumor-suppressor p53 and the E3-ligase MDM2. We virtually screened a library of 15 million small molecules that were filtered to a final set of 80 virtual hits. Our in vitro experimental assay, designed to validate the activity of mixtures of compounds by isothermal titration calorimetry, was used to identify an active molecule against MDM2. At the end of the process the small molecule (4S,7R)-4-(4-chlorophenyl)-5-hydroxy-2,7-dimethyl-N-(6-methylpyridin-2-yl)-4,6,7,8 tetrahydrIoquinoline-3-carboxamide was found to bind MDM2 with a dissociation constant of ~2 µM. Following the identification of this single bioactive compound, spectroscopic measurements were used to further characterize the interaction of the small molecule with the target protein. 2D NMR spectroscopy was used to map the binding region of the small molecule, and fluorescence polarization measurement confirmed that it indeed competes with p53.

  6. The rate of collisions due to Brownian or gravitational motion of small drops

    Science.gov (United States)

    Zhang, Xiaoguang; Davis, Robert H.

    1991-01-01

    Quantitative predictions of the collision rate of two spherical drops undergoing Brownian diffusion or gravitational sedimentation are presented. The diffusion equation for relative Brownian motion of two drops is derived, and the relative motion of pairs of drops in gravitational sedimentation is traced via a trajectory analysis in order to develop theoretical models to determine the collision efficiencies, both with and without interparticle forces applied between the drops. It is concluded that finite collision rates between nondeforming fluid drops are possible for Brownian diffusion or gravitational sedimentation in the absence of attractive forces, in stark contrast to the prediction that lubrication forces prevent rigid spheres from contacting each other unless an attractive force that becomes infinite as the separation approaches zero is applied. Collision rates are shown to increase as the viscosity of the drop-phase decreases. In general, hydrodynamic interactions reduce the collision rates more for gravitational collisions than for Brownian collisions.

  7. Calculation of microscopic exchange interactions and modelling of macroscopic magnetic properties in molecule-based magnets.

    Science.gov (United States)

    Novoa, J J; Deumal, M; Jornet-Somoza, J

    2011-06-01

    The state-of-the-art theoretical evaluation and rationalization of the magnetic interactions (J(AB)) in molecule-based magnets is discussed in this critical review, focusing first on isolated radical···radical pair interactions and afterwards on how these interactions cooperate in the solid phase. Concerning isolated radical pairwise magnetic interactions, an initial analysis is done on qualitative grounds, concentrating also on the validity of the most commonly used models to predict their size and angularity (namely, McConnell-I and McConnell-II models, overlap of magnetic orbitals,…). The failure of these models, caused by their oversimplified description of the magnetic interactions, prompted the introduction of quantitative approaches, whose basic principles and relative quality are also evaluated. Concerning the computation of magnetic interactions in solids, we resort to a sum of pairwise magnetic interactions within the Heisenberg Hamiltonian framework, and follow the First-principles Bottom-Up procedure, which allows the accurate study of the magnetic properties of any molecule-based magnet in an unbiased way. The basic principles of this approach are outlined, applied in detail to a model system, and finally demonstrated to properly describe the magnetic properties of molecule-based systems that show a variety of magnetic topologies, which range from 1D to 3D (152 references).

  8. Oncogene Expression Modulation in Cancer Cell Lines by DNA G-Quadruplex-Interactive Small Molecules.

    Science.gov (United States)

    Francisco, Ana Paula; Paulo, Alexandra

    2017-01-01

    Nucleic acids are prone to structural polymorphism and a number of structures may be formed in addition to the well-known DNA double helix. Among these is a family of nucleic acid four-stranded structures known as G-quadruplexes (G4). These quadruplex structures can be formed by sequences containing repetitive guanine-rich tracks and the analysis of Non-B-DNA database indicated an enrichment of these sequences in genomic regions controlling cellular proliferation, such as for example in the promoter regions of c- MYC, k-RAS, c-KIT, HSP90 and VEGF among others. The broad concept of G4 targeting with small molecules is now generally accepted as a promising novel approach to anticancer therapy and several small molecules with antiproliferative activity in cancer cell lines have also been shown to stabilize these DNA structures, thus suggesting a potential application of G4-interactive small molecules as new anticancer drugs. Herein we review, by targeted oncogene and main chemical scaffold, those G4-interactive small molecules with reported gene expression modulatory activity in cancer cell lines. The data obtained so far are encouraging but further efforts are needed to validate G4 as drug targets and optimize the structure of G4- interactive small molecules into new anticancer drugs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  9. DFT study on the interaction of TiO2 (001) surface with HCHO molecules

    Science.gov (United States)

    Wu, Guofei; Zhao, Cuihua; Guo, Changqing; Chen, Jianhua; Zhang, Yibing; Li, Yuqiong

    2018-01-01

    The interactions of formaldehyde (HCHO) molecule with TiO2 (001) surface were studied using density functional theory calculations. HCHO molecules are dissociated by the cleavage of Csbnd H bonds after adsorption on TiO2 surface. The strong interactions between HCHO melecules and TiO2 surface are largely attributed to the bonding of hydrogen of HCHO and oxygen of TiO2 surface, which is mainly from the hybridization of the H 1s, O 2p and O 2s. The newly formed Hsbnd O bonds cause the structure changes of TiO2 surface, and lead to the cleavage of Osbnd Ti bond of TiO2 surface. The Csbnd O bond that the dissociated remains of HCHO and newly formed Hsbnd O bond can be oxidized to form carbon dioxide and water in subsequent action by oxygen from the atomosphere. The charges transfer from HCHO to TiO2 surface, and the sum amount of the charges transferred from four HCHO molecules to TiO2 surface is bigger than that from one HCHO molecule to TiO2 surface due to the combined interaction of four HCHO molecules with TiO2 surface.

  10. Non-relativistic treatment of diatomic molecules interacting with a generalized Kratzer potential in hyperspherical coordinates

    International Nuclear Information System (INIS)

    Durmus, Aysen

    2011-01-01

    We investigate solutions of a non-relativistic wave equation in hyperspherical coordinates for a diatomic molecule system interacting with a generalized Kratzer potential. Rovibrational eigenvalues and corresponding wavefunctions of non-relativistic diatomic molecules have been determined within the framework of the asymptotic iteration method. Certain fundamental conditions for the applications of the asymptotic iteration method, such as a suitable asymptotic form for the wave-function and the termination condition for the iteration process, are discussed. N-dimensional bound state eigenfunction solutions used in studying the dynamical variables of diatomic molecules are obtained in terms of a confluent hypergeometric function and a generalized Laguerre polynomial. This systematic approach is tested by calculating the rovibrational energy spectra of hydrogen and sodium chloride molecules.

  11. Single-Molecule Sensing with Nanopore Confinement: from Chemical Reactions to Biological Interactions.

    Science.gov (United States)

    Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

    2018-03-25

    The nanopore can generate an electrochemical confinement for single-molecule sensing which help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this concept, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. EVAPORATION: a new vapour pressure estimation methodfor organic molecules including non-additivity and intramolecular interactions

    Science.gov (United States)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-09-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict (subcooled) liquid pure compound vapour pressure p0 of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  13. Brownian motion - a laboratory experiment

    Science.gov (United States)

    Kruglak, Haym

    1988-09-01

    The availability of latex microspheres, compact television cameras and electronic calculators make it possible to perform an experiment on Brownian movement in one laboratory period. A more accurate value of N can be determined by other methods. However, the experiment described above has several valuable pedagogical outcomes. Undergraduate students get experience with several experimental techniques: (i) recording a `random walk' of a microphere; (ii) plotting a histogram of displacements; (iii) fitting a Gaussian curve to the histogram; (iv) checking the goodness of fit analytically or with probability graph paper; (v) calibrating screen displacements with a diffraction grating; (vi) calculating Avogadro's number from the experimental data; (vii) verifying data validity with the Einstein - Smoluchowski Law. The experiment also provides valuable practice in unit conversion and error analysis. Another instructive feature: the experiment makes the students aware of Einstein's work other than relativity. The students' reactions to the experiment were positive: `interesting', `challenging', `fun'.

  14. Interaction of the Explosive Molecules RDX and TATP with IRMOF-8

    Energy Technology Data Exchange (ETDEWEB)

    Odbadrakh, Khorgolkhuu [ORNL; Lewis, James [West Virginia University; Nicholson, Don M [ORNL

    2010-01-01

    We report our investigations on physisorption and trapping of high explosive (HE) molecules 1,3,5-trinitro-s-triazine or cyclotrimethylene trinitramine (RDX) and triacetone triperoxide (TATP) by an isoreticular metal-organic framework (IRMOF) IRMOF-8. In general, IRMOFs are known for their high porosity and tailorability, thus having potential applications as preconcentrators, and gas storage. In particular, IRMOF-8 has higher hydrogen uptake than the extensively studied IRMOF-1, thus having the potential to act as preconcentrators for explosive molecules. We employed the ab initio density functional theory (DFT) code FIREBALL to estimate physisorption interactions for the RDX and TATP molecules with interior and exterior surfaces of IRMOF-8. At zero temperature, RDX yields several physisorption type binding configurations, while TATP remains more inert to interactions with IRMOF-8. Molecular dynamics simulations at room temperature result in trapping configurations preferring TATP inside the IRMOF-8 cage, which could be attributed to molecular sieving effects.

  15. Synchronization and collective motion of globally coupled Brownian particles

    International Nuclear Information System (INIS)

    Sevilla, Francisco J; Heiblum-Robles, Alexandro; Dossetti, Victor

    2014-01-01

    In this work, we study a system of passive Brownian (non-self-propelled) particles in two dimensions, interacting only through a social-like force (velocity alignment in this case) that resembles Kuramoto's coupling among phase oscillators. We show that the kinematical stationary states of the system go from a phase in thermal equilibrium with no net flux of particles, to far-from-equilibrium phases exhibiting collective motion by increasing the coupling among particles. The mechanism that leads to the instability of the equilibrium phase relies on the competition between two time scales, namely, the mean collision time of the Brownian particles in a thermal bath and the time it takes for a particle to orient its direction of motion along the direction of motion of the group. Our results show a clear connection between collective motion and the Kuramoto model for synchronization, in our case, for the direction of motion of the particles. (paper)

  16. Interactively Applying the Variational Method to the Dihydrogen Molecule: Exploring Bonding and Antibonding

    Science.gov (United States)

    Cruzeiro, Vinícius Wilian D.; Roitberg, Adrian; Polfer, Nicolas C.

    2016-01-01

    In this work we are going to present how an interactive platform can be used as a powerful tool to allow students to better explore a foundational problem in quantum chemistry: the application of the variational method to the dihydrogen molecule using simple Gaussian trial functions. The theoretical approach for the hydrogen atom is quite…

  17. Interactions of the humoral pattern recognition molecule PTX3 with the complement system

    DEFF Research Database (Denmark)

    Doni, Andrea; Garlanda, Cecilia; Bottazzi, Barbara

    2012-01-01

    The innate immune system comprises a cellular and a humoral arm. The long pentraxin PTX3 is a fluid phase pattern recognition molecule, which acts as an essential component of the humoral arm of innate immunity. PTX3 has antibody-like properties including interactions with complement components...

  18. Stock price prediction using geometric Brownian motion

    Science.gov (United States)

    Farida Agustini, W.; Restu Affianti, Ika; Putri, Endah RM

    2018-03-01

    Geometric Brownian motion is a mathematical model for predicting the future price of stock. The phase that done before stock price prediction is determine stock expected price formulation and determine the confidence level of 95%. On stock price prediction using geometric Brownian Motion model, the algorithm starts from calculating the value of return, followed by estimating value of volatility and drift, obtain the stock price forecast, calculating the forecast MAPE, calculating the stock expected price and calculating the confidence level of 95%. Based on the research, the output analysis shows that geometric Brownian motion model is the prediction technique with high rate of accuracy. It is proven with forecast MAPE value ≤ 20%.

  19. The origins of life -- the 'protein interaction world' hypothesis: protein interactions were the first form of self-reproducing life and nucleic acids evolved later as memory molecules.

    Science.gov (United States)

    Andras, Peter; Andras, Csaba

    2005-01-01

    The 'protein interaction world' (PIW) hypothesis of the origins of life assumes that life emerged as a self-reproducing and expanding system of protein interactions. In mainstream molecular biology, 'replication' refers to the material copying of molecules such as nucleic acids. However, PIW is conceptualized as an abstract communication system constituted by the interactions between proteins, in which 'replication' happens at the level of self-reproduction of these interactions between proteins. Densely concentrated peptide interaction systems may have reproduced and expanded as 'protocell' vesicles surrounded by lipid bi-layer membranes. Protocells led to the emergence of proto-RNA molecules of greater chemical stability which served as chemically differentiated 'memories' of peptide interaction states, thereby facilitating the reproduction and expansion of protocells. Simplification-driven expansion led to the selection of biotic amino acids and the reduction of the typical RNA alphabet to the four usual bases (A, C, G and U). Dense interactions between RNA molecules led to the emergence of the RNA interaction subsystem of the cell, and to the emergence of 'memories' of RNA interactions in the form of DNA molecules with greater chemical stability. The expansion of DNA molecule interactions led to the dense clustering and encapsulation of DNA molecules within the cell nucleus. RNA molecules therefore serve as memories of protein interactions and DNA molecules are memories of RNA interactions. We believe that the PIW hypothesis is more evolutionarily plausible than the mainstream RNA world hypothesis, and has greater explanatory power.

  20. Methylobacterium-plant interaction genes regulated by plant exudate and quorum sensing molecules

    Directory of Open Access Journals (Sweden)

    Manuella Nóbrega Dourado

    2013-12-01

    Full Text Available Bacteria from the genus Methylobacterium interact symbiotically (endophytically and epiphytically with different plant species. These interactions can promote plant growth or induce systemic resistance, increasing plant fitness. The plant colonization is guided by molecular communication between bacteria-bacteria and bacteria-plants, where the bacteria recognize specific exuded compounds by other bacteria (e.g. homoserine molecules and/or by the plant roots (e.g. flavonoids, ethanol and methanol, respectively. In this context, the aim of this study was to evaluate the effect of quorum sensing molecules (N-acyl-homoserine lactones and plant exudates (including ethanol in the expression of a series of bacterial genes involved in Methylobacterium-plant interaction. The selected genes are related to bacterial metabolism (mxaF, adaptation to stressful environment (crtI, phoU and sss, to interactions with plant metabolism compounds (acdS and pathogenicity (patatin and phoU. Under in vitro conditions, our results showed the differential expression of some important genes related to metabolism, stress and pathogenesis, thereby AHL molecules up-regulate all tested genes, except phoU, while plant exudates induce only mxaF gene expression. In the presence of plant exudates there is a lower bacterial density (due the endophytic and epiphytic colonization, which produce less AHL, leading to down regulation of genes when compared to the control. Therefore, bacterial density, more than plant exudate, influences the expression of genes related to plant-bacteria interaction.

  1. Methylobacterium-plant interaction genes regulated by plant exudate and quorum sensing molecules

    Science.gov (United States)

    Dourado, Manuella Nóbrega; Bogas, Andrea Cristina; Pomini, Armando M.; Andreote, Fernando Dini; Quecine, Maria Carolina; Marsaioli, Anita J.; Araújo, Welington Luiz

    2013-01-01

    Bacteria from the genus Methylobacterium interact symbiotically (endophytically and epiphytically) with different plant species. These interactions can promote plant growth or induce systemic resistance, increasing plant fitness. The plant colonization is guided by molecular communication between bacteria-bacteria and bacteria-plants, where the bacteria recognize specific exuded compounds by other bacteria (e.g. homoserine molecules) and/or by the plant roots (e.g. flavonoids, ethanol and methanol), respectively. In this context, the aim of this study was to evaluate the effect of quorum sensing molecules (N-acyl-homoserine lactones) and plant exudates (including ethanol) in the expression of a series of bacterial genes involved in Methylobacterium-plant interaction. The selected genes are related to bacterial metabolism (mxaF), adaptation to stressful environment (crtI, phoU and sss), to interactions with plant metabolism compounds (acdS) and pathogenicity (patatin and phoU). Under in vitro conditions, our results showed the differential expression of some important genes related to metabolism, stress and pathogenesis, thereby AHL molecules up-regulate all tested genes, except phoU, while plant exudates induce only mxaF gene expression. In the presence of plant exudates there is a lower bacterial density (due the endophytic and epiphytic colonization), which produce less AHL, leading to down regulation of genes when compared to the control. Therefore, bacterial density, more than plant exudate, influences the expression of genes related to plant-bacteria interaction. PMID:24688531

  2. Small-molecule stabilization of the p53 - 14-3-3 protein-protein interaction.

    Science.gov (United States)

    Doveston, Richard G; Kuusk, Ave; Andrei, Sebastian A; Leysen, Seppe; Cao, Qing; Castaldi, Maria P; Hendricks, Adam; Brunsveld, Luc; Chen, Hongming; Boyd, Helen; Ottmann, Christian

    2017-08-01

    14-3-3 proteins are positive regulators of the tumor suppressor p53, the mutation of which is implicated in many human cancers. Current strategies for targeting of p53 involve restoration of wild-type function or inhibition of the interaction with MDM2, its key negative regulator. Despite the efficacy of these strategies, the alternate approach of stabilizing the interaction of p53 with positive regulators and, thus, enhancing tumor suppressor activity, has not been explored. Here, we report the first example of small-molecule stabilization of the 14-3-3 - p53 protein-protein interaction (PPI) and demonstrate the potential of this approach as a therapeutic modality. We also observed a disconnect between biophysical and crystallographic data in the presence of a stabilizing molecule, which is unusual in 14-3-3 PPIs. © 2017 Federation of European Biochemical Societies.

  3. DNA electrophoresis in tri-block copolymer gels--experiments and Brownian dynamics simulation

    Science.gov (United States)

    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.

  4. Interaction of water molecules with hexagonal 2D systems. A DFT study

    Science.gov (United States)

    Rojas, Ángela; Rey, Rafael

    Over the years water sources have been contaminated with many chemical agents, becoming issues that affect health of the world population. The advances of the nanoscience and nanotechnology in the development new materials constitute an alternative for design molecular filters with great efficiencies and low cost for water treatment and purification. In the nanoscale, the process of filtration or separation of inorganic and organic pollutants from water requires to study interactions of these atoms or molecules with different nano-materials. Specifically, it is necessary to understand the role of these interactions in physical and chemical properties of the nano-materials. In this work, the main interest is to do a theoretical study of interaction between water molecules and 2D graphene-like systems, such as silicene (h-Si) or germanene (h-Ge). Using Density Functional Theory we calculate total energy curves as function of separation between of water molecules and 2D systems. Different spatial configurations of water molecules relative to 2D systems are considered. Structural relaxation effects and changes of electronic charge density also are reported. Universidad Nacional de Colombia.

  5. On some generalization of fractional Brownian motions

    Energy Technology Data Exchange (ETDEWEB)

    Wang Xiaotian [School of Management, Tianjin University, Tianjin 300072 (China); Liang Xiangqian [Department of Applied Mathematics, Shandong University of Science and Technology, Qingdao 266510, Shandong (China); Ren Fuyao [Institute of Mathematics, Fudan University, Shanghai 200433 (China); Zhang Shiying [School of Management, Tianjin University, Tianjin 300072 (China)]. E-mail: swa001@126.com

    2006-05-15

    The multifractional Brownian motion (mBm) is a continuous Gaussian process that extends the classical fractional Brownian motion (fBm) defined by Barton and Vincent Poor [Barton RJ, Vincent Poor H. IEEE Trans Inform 1988;34(5):943] and Decreusefond and Ustuenel [Decreusefond L, Ustuenel AS. Potential Anal 1999;10:177]. In addition, an innovational representation of fBm is given.

  6. Brownian motion after Einstein and Smoluchowski: Some new applications and new experiments

    DEFF Research Database (Denmark)

    Dávid, Selmeczi; Tolic-Nørrelykke, S.F.; Schäffer, E.

    2007-01-01

    that it requires an understanding of Brownian motion beyond Einstein's and Smoluchowski's for its calibration, and can measure effects not present in their theories. This is illustrated with some applications, current and potential. It is also shown how addition of a controlled forced motion on the nano......The first half of this review describes the development in mathematical models of Brownian motion after Einstein's and Smoluchowski's seminal papers and current applications to optical tweezers. This instrument of choice among single-molecule biophysicists is also an instrument of such precision...

  7. Brownian motion after Einstein and Smoluchowski: Some new applications and new experiments

    DEFF Research Database (Denmark)

    Dávid, Selmeczi; Tolic-Nørrelykke, S.F.; Schäffer, E.

    2007-01-01

    The first half of this review describes the development in mathematical models of Brownian motion after Einstein's and Smoluchowski's seminal papers and current applications to optical tweezers. This instrument of choice among single-molecule biophysicists is also an instrument of such precision...... that it requires an understanding of Brownian motion beyond Einstein's and Smoluchowski's for its calibration, and can measure effects not present in their theories. This is illustrated with some applications, current and potential. It is also shown how addition of a controlled forced motion on the nano...

  8. Interaction of an immunodominant epitope with Ia molecules in T-cell activation

    DEFF Research Database (Denmark)

    Adorini, L; Sette, A; Buus, S

    1988-01-01

    but not the binding to I-Ed molecules, whereas, as shown by binding data and competition experiments, an Arg----His substitution at position 114 profoundly impairs the capacity of the peptide to interact with I-Ed molecules. In agreement with these results, [Lys113]HEL-(105-120)-peptide but not [His114]HEL-(105......-120)-peptide binds to I-Ed but not to I-Ad molecules. Conservative or semiconservative substitutions at positions 113 (Asn----Lys), 114 (Arg----His), or 115 (Cys----Ala) abrogate the ability of HEL-(105-120) to activate T cells. Substitutions at residues 113 and 115 affect T-cell recognition...

  9. Interactions of gas molecules with monolayer MoSe{sub 2}: A first principle study

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Munish, E-mail: munishsharmahpu@live.com; Jamdagni, Pooja; Ahluwalia, P. K. [Department. of Physics, Himachal Pradesh University, Shimla, H. P., 171005 (India); Kumar, Ashok [Centre for Physical Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001(India)

    2016-05-23

    We present a first principle study of interaction of toxic gas molecules (NO, NO{sub 2} and SO{sub 2}) with monolayer MoSe{sub 2}. The predicted order of sensitivity of gas molecule is NO{sub 2} > SO{sub 2} > NO. Adsorbed molecules strongly influence the electronic behaviour of monolayer MoSe{sub 2} by inducing impurity levels in the vicinity of Fermi energy. NO and SO{sub 2} is found to induce p-type doping effect while semiconductor to metallic transitions occur on NO{sub 2} adsorption. Our findings may guide the experimentalist for fabricating sensor devices based on MoSe{sub 2} monolayer.

  10. Biophysics of DNA-Protein Interactions From Single Molecules to Biological Systems

    CERN Document Server

    Williams, Mark C

    2011-01-01

    This book presents a concise overview of current research on the biophysics of DNA-protein interactions. A wide range of new and classical methods are presented by authors investigating physical mechanisms by which proteins interact with DNA. For example, several chapters address the mechanisms by which proteins search for and recognize specific binding sites on DNA, a process critical for cellular function. Single molecule methods such as force spectroscopy as well as fluorescence imaging and tracking are described in these chapters as well as other parts of the book that address the dynamics of protein-DNA interactions. Other important topics include the mechanisms by which proteins engage DNA sequences and/or alter DNA structure. These simple but important model interactions are then placed in the broader biological context with discussion of larger protein-DNA complexes . Topics include replication forks, recombination complexes, DNA repair interactions, and ultimately, methods to understand the chromatin...

  11. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Osiry, H.; Cano, A.; Lemus-Santana, A.A.; Rodríguez, A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional (Mexico); Carbonio, R.E. [INFIQC-CONICET, Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba (Argentina); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional (Mexico)

    2015-10-15

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.

  12. Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure.

    Science.gov (United States)

    Takeuchi, Yosuke; Endo, Masayuki; Suzuki, Yuki; Hidaka, Kumi; Durand, Guillaume; Dausse, Eric; Toulmé, Jean-Jacques; Sugiyama, Hiroshi

    2016-01-01

    RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.

  13. Equilibrium stochastic dynamics of a Brownian particle in inhomogeneous space: Derivation of an alternative model

    Science.gov (United States)

    Bhattacharyay, A.

    2018-03-01

    An alternative equilibrium stochastic dynamics for a Brownian particle in inhomogeneous space is derived. Such a dynamics can model the motion of a complex molecule in its conformation space when in equilibrium with a uniform heat bath. The derivation is done by a simple generalization of the formulation due to Zwanzig for a Brownian particle in homogeneous heat bath. We show that, if the system couples to different number of bath degrees of freedom at different conformations then the alternative model gets derived. We discuss results of an experiment by Faucheux and Libchaber which probably has indicated possible limitation of the Boltzmann distribution as equilibrium distribution of a Brownian particle in inhomogeneous space and propose experimental verification of the present theory using similar methods.

  14. Hydrogen sulphide in cardiovascular system: A cascade from interaction between sulphur atoms and signalling molecules.

    Science.gov (United States)

    Wang, Ming-Jie; Cai, Wen-Jie; Zhu, Yi-Chun

    2016-05-15

    As a gasotransmitter, hydrogen sulphide exerts its extensive physiological and pathophysiological effects in mammals. The interaction between sulphur atoms and signalling molecules forms a cascade that modulates cellular functions and homeostasis. In this review, we focus on the signalling mechanism underlying the effect of hydrogen sulphide in the cardiovascular system and metabolism as well as the biological relevance to human diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Nature of chalcogen hor ellipsis chalcogen contact interactions in organic donor-molecule salts

    Energy Technology Data Exchange (ETDEWEB)

    Novoa, J.J.; Whangbo, Myung-Hwan (North Carolina State Univ., Raleigh, NC (USA). Dept. of Chemistry); Williams, J.M. (Argonne National Lab., IL (USA))

    1990-01-01

    The nature of chalcogen{hor ellipsis}chalcogen contact interactions in organic donor-molecule salts was examined by performing ab initio SCF-MO/MP2 calculations on H{sub 2}X{hor ellipsis}XH{sub 2}(X = O, S, SE, Te) and MM2 calculations on donor dimers (TXF){sub 2} (X = S, SE, Te) and (BEDX-TTF){sub 2} (X = O, S). 14 refs., 4 figs., 4 tabs.

  16. Managing light polarization via plasmon-molecule interactions within an asymmetric metal nanoparticle trimer

    International Nuclear Information System (INIS)

    Shegai, Timur; Li, Zhipeng; Zhang, Zhenyu; Xu, Hongxing; Haran, Gilad

    2008-01-01

    The interaction of light with metal nanoparticles leads to novel phenomena mediated by surface plasmon excitations. In this paper we use single molecules to characterize the interaction of surface plasmons with light, and show that such interaction can strongly modulate the polarization of the emitted light. The simplest nanostructures that enable such polarization modulation are asymmetric silver nanocrystal trimers, where individual Raman scattering molecules are located in the gap between two of the nanoparticles. The third particle breaks the dipolar symmetry of the two-particle junction, generating a wavelength-dependent polarization pattern. Indeed, the scattered light becomes elliptically polarized and its intensity pattern is rotated in the presence of the third particle. We use a combination of spectroscopic observations on single molecules, scanning electron microscope imaging, and generalized Mie theory calculations to provide a full picture of the effect of particles on the polarization of the emitted light. Furthermore, our theoretical analysis allows us to show that the observed phenomenon is very sensitive to the size of the trimer particles and their relative position, suggesting future means for precise control of light polarization on the nanoscale.

  17. Structural Analysis of ‘key’ Interactions in Functional RNA Molecules

    KAUST Repository

    Chawla, Mohit

    2018-04-01

    The main objective of the thesis is to carry out structural bioinformatics study along with usage of advanced quantum chemical methods to look at the structural stability and energetics of RNA building blocks. The main focus of the work described here lies on understanding the reasons behind the intrinsic stability of key interactions in nucleic acids. Crystal structures of RNA molecules exhibit fascinating variety of non-covalent interactions, which play an important role in maintaining the three dimensional structures. An accurate atomic level description of these interactions in the structural building blocks of RNA is a key to understand the structure-function relationship in these molecules. An effort has been made to link the conclusions drawn from quantum chemical computations on RNA base pairs in wide biochemical context of their occurrence in RNA structures. The initial attention was on the impact of natural and non-natural modifications of the nucleic acid bases on the structure and stability of base pairs that they are involved in. In the remaining sections we cover other molecular interactions shaping nucleic acids, as the interaction between ribose and the bases, and the fluoride sensing riboswitch system in order to investigate structure and dynamics of nucleic acids at the atomic level and to gain insight into the physical chemistry behind.

  18. Single molecule DNA interaction kinetics of retroviral nucleic acid chaperone proteins

    Science.gov (United States)

    Williams, Mark

    2010-03-01

    Retroviral nucleocapsid (NC) proteins are essential for several viral replication processes including specific genomic RNA packaging and reverse transcription. The nucleic acid chaperone activity of NC facilitates the latter process. In this study, we use single molecule biophysical methods to quantify the DNA interactions of wild type and mutant human immunodeficiency virus type 1 (HIV-1) NC and Gag and human T-cell leukemia virus type 1 (HTLV-1) NC. We find that the nucleic acid interaction properties of these proteins differ significantly, with HIV-1 NC showing rapid protein binding kinetics, significant duplex destabilization, and strong DNA aggregation, all properties that are critical components of nucleic acid chaperone activity. In contrast, HTLV-1 NC exhibits significant destabilization activity but extremely slow DNA interaction kinetics and poor aggregating capability, which explains why HTLV-1 NC is a poor nucleic acid chaperone. To understand these results, we developed a new single molecule method for quantifying protein dissociation kinetics, and applied this method to probe the DNA interactions of wild type and mutant HIV-1 and HTLV-1 NC. We find that mutations to aromatic and charged residues strongly alter the proteins' nucleic acid interaction kinetics. Finally, in contrast to HIV-1 NC, HIV-1 Gag, the nucleic acid packaging protein that contains NC as a domain, exhibits relatively slow binding kinetics, which may negatively impact its ability to act as a nucleic acid chaperone.

  19. Confined Catalysis in the g-C3N4/Pt(111) Interface: Feasible Molecule Intercalation, Tunable Molecule-Metal Interaction, and Enhanced Reaction Activity of CO Oxidation.

    Science.gov (United States)

    Wang, Shujiao; Feng, Yingxin; Yu, Ming'an; Wan, Qiang; Lin, Sen

    2017-09-27

    The deposition of a two-dimensional (2D) atomic nanosheet on a metal surface has been considered as a new route for tuning the molecule-metal interaction and surface reactivity in terms of the confinement effect. In this work, we use first-principles calculations to systematically explore a novel nanospace constructed by placing a 2D graphitic carbon nitride (g-C 3 N 4 ) nanosheet over a Pt(111) surface. The confined catalytic activity in this nanospace is investigated using CO oxidation as a model reaction. With the inherent triangular pores in the g-C 3 N 4 overlayer being taken advantage of, molecules such as CO and O 2 can diffuse to adsorb on the Pt(111) surface underneath the g-C 3 N 4 overlayer. Moreover, the mechanism of intercalation is also elucidated, and the results reveal that the energy barrier depends mainly on the properties of the molecule and the channel. Importantly, the molecule-catalyst interaction can be tuned by the g-C 3 N 4 overlayer, considerably reducing the adsorption energy of CO on Pt(111) and leading to enhanced reactivity in CO oxidation. This work will provide important insight for constructing a promising nanoreactor in which the following is observed: The molecule intercalation is facile; the molecule-metal interaction is efficiently tuned; the metal-catalyzed reaction is promoted.

  20. STITCH 2: an interaction network database for small molecules and proteins

    DEFF Research Database (Denmark)

    Kuhn, Michael; Szklarczyk, Damian; Franceschini, Andrea

    2010-01-01

    Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug......-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other...... chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/....

  1. Generalized Fokker-Planck equation, Brownian motion, and ergodicity.

    Science.gov (United States)

    Plyukhin, A V

    2008-06-01

    Microscopic theory of Brownian motion of a particle of mass M in a bath of molecules of mass mforce, and the generalized Fokker-Planck equation involves derivatives of order higher than 2. These equations are derived from first principles with coefficients expressed in terms of correlation functions of microscopic force on the particle. The coefficients are evaluated explicitly for a generalized Rayleigh model with a finite time of molecule-particle collisions. In the limit of a low-density bath, we recover the results obtained previously for a model with instantaneous binary collisions. In the general case, the equations contain additional corrections, quadratic in bath density, originating from a finite collision time. These corrections survive to order (m/M)2 and are found to make the stationary distribution non-Maxwellian. Some relevant numerical simulations are also presented.

  2. Single NdPc2 molecules on surfaces. Adsorption, interaction, and molecular magnetism

    International Nuclear Information System (INIS)

    Fahrendorf, Sarah

    2013-01-01

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc 2 ) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc 2 ) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc 2 molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the spin

  3. Single NdPc{sub 2} molecules on surfaces. Adsorption, interaction, and molecular magnetism

    Energy Technology Data Exchange (ETDEWEB)

    Fahrendorf, Sarah

    2013-01-24

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc{sub 2}) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc{sub 2}) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc{sub 2} molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the

  4. EVAPORATION: a new vapour pressure estimation methodfor organic molecules including non-additivity and intramolecular interactions

    Directory of Open Access Journals (Sweden)

    S. Compernolle

    2011-09-01

    Full Text Available We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects, a method to predict (subcooled liquid pure compound vapour pressure p0 of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA.

  5. c-Met and Other Cell Surface Molecules: Interaction, Activation and Functional Consequences

    Directory of Open Access Journals (Sweden)

    Giuditta Viticchiè

    2015-01-01

    Full Text Available The c-Met receptor, also known as the HGF receptor, is one of the most studied tyrosine kinase receptors, yet its biological functions and activation mechanisms are still not fully understood. c-Met has been implicated in embryonic development and organogenesis, in tissue remodelling homeostasis and repair and in cancer metastasis. These functions are indicative of the many cellular processes in which the receptor plays a role, including cell motility, scattering, survival and proliferation. In the context of malignancy, sustained activation of c-Met leads to a signalling cascade involving a multitude of kinases that initiate an invasive and metastatic program. Many proteins can affect the activation of c-Met, including a variety of other cell surface and membrane-spanning molecules or receptors. Some cell surface molecules share structural homology with the c-Met extracellular domain and can activate c-Met via clustering through this domain (e.g., plexins, whereas other receptor tyrosine kinases can enhance c-Met activation and signalling through intracellular signalling cascades (e.g., EGFR. In this review, we provide an overview of c-Met interactions and crosstalk with partner molecules and the functional consequences of these interactions on c-Met activation and downstream signalling, c-Met intracellular localization/recycling and c-Met degradation.

  6. In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction.

    Science.gov (United States)

    Randjelovic, Jelena; Eric, Slavica; Savic, Vladimir

    2014-05-01

    In order to design a small molecule which potentially may interfere with CDK9/cyclin T1 complex formation and therefore influence its physiological role, a computational study of dynamics and druggability of CDK9 binding surface was conducted. Druggability estimates and pocket opening analyses indicated binding regions of cyclin T1 residues, Phe 146 and Lys 6, as starting points for the design of small molecules with the potential to inhibit the CDK9/cyclin T1 association. A pharmacophore model was created, based on these two residues and used to select potential inhibitor structures. Binding energies of the inhibitors were estimated with MM-GBSA. A good correlation of MM-GBSA energies and FTMap druggability predictions was observed. Amongst studied compounds a derivative of 2-amino-8-hydroxyquinoline was identified as the best potential candidate to inhibit CDK9/cyclin T1 interactions. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Single Molecule Study on Polymer-Nanoparticle Interactions: The Particle Shape Matters.

    Science.gov (United States)

    Li, Zhandong; Zhang, Bin; Song, Yu; Xue, Yurui; Wu, Lixin; Zhang, Wenke

    2017-08-08

    The study on the nanoparticle-polymer interactions is very important for the design/preparation of high performance polymer nanocomposite. Here we present a method to quantify the polymer-particle interaction at single molecule level by using AFM-based single molecule force spectroscopy (SMFS). As a proof-of-concept study, we choose poly-l-lysine (PLL) as the polymer and several different types of polyoxometalates (POM) as the model particles to construct several different polymer nanocomposites and to reveal the binding mode and quantify the binding strength in these systems. Our results reveal that the shape of the nanoparticle and the binding geometry in the composite have significantly influenced the binding strength of the PLL/POM complexes. Our dynamic force spectroscopy studies indicate that the disk-like geometry facilitate the unbinding of PLL/AlMo 6 complexes in shearing mode, while the unzipping mode becomes dominate in spherical PLL-P 8 W 48 system. We have also systematically investigated the effects of charge numbers, particle size, and ionic strength on the binding strength and binding mode of PLL/POM, respectively. Our results show that electrostatic interactions dominate the stability of PLL/POM complexes. These findings provide a way for tuning the mechanical properties of polyelectrolyte-nanoparticle composites.

  8. Self-interaction corrections applied to Mg-porphyrin, C60, and pentacene molecules

    International Nuclear Information System (INIS)

    Pederson, Mark R.; Baruah, Tunna; Basurto, Luis; Kao, Der-you

    2016-01-01

    We have applied a recently developed method to incorporate the self-interaction correction through Fermi orbitals to Mg-porphyrin, C 60 , and pentacene molecules. The Fermi-Löwdin orbitals are localized and unitarily invariant to the Kohn-Sham orbitals from which they are constructed. The self-interaction-corrected energy is obtained variationally leading to an optimum set of Fermi-Löwdin orbitals (orthonormalized Fermi orbitals) that gives the minimum energy. A Fermi orbital, by definition, is dependent on a certain point which is referred to as the descriptor position. The degree to which the initial choice of descriptor positions influences the variational approach to the minimum and the complexity of the energy landscape as a function of Fermi-orbital descriptors is examined in detail for Mg-porphyrin. The applications presented here also demonstrate that the method can be applied to larger molecular systems containing a few hundred electrons. The atomization energy of the C 60 molecule within the Fermi-Löwdin-orbital self-interaction-correction approach is significantly improved compared to local density approximation in the Perdew-Wang 92 functional and generalized gradient approximation of Perdew-Burke-Ernzerhof functionals. The eigenvalues of the highest occupied molecular orbitals show qualitative improvement.

  9. Single-Molecule Characterization of DNA-Protein Interactions Using Nanopore Biosensors.

    Science.gov (United States)

    Squires, A H; Gilboa, T; Torfstein, C; Varongchayakul, N; Meller, A

    2017-01-01

    Detection and characterization of nucleic acid-protein interactions, particularly those involving DNA and proteins such as transcription factors, enzymes, and DNA packaging proteins, remain significant barriers to our understanding of genetic regulation. Nanopores are an extremely sensitive and versatile sensing platform for label-free detection of single biomolecules. Analyte molecules are drawn to and through a nanoscale aperture by an electrophoretic force, which acts upon their native charge while in the sensing region of the pore. When the nanopore's diameter is only slightly larger than the biopolymer's cross section (typically a few nm); the latter must translocate through the pore in a linear fashion due to the constricted geometry in this region. These features allow nanopores to interrogate protein-nucleic acids in multiple sensing modes: first, by scanning and mapping the locations of binding sites along an analyte molecule, and second, by probing the strength of the bond between a protein and nucleic acid, using the native charge of the nucleic acid to apply an electrophoretic force to the complex while the protein is geometrically prevented from passing through the nanopore. In this chapter, we describe progress toward nanopore sensing of protein-nucleic acid complexes in the context of both mapping binding sites and performing force spectroscopy to determine the strength of interactions. We conclude by reviewing the strengths and challenges of the nanopore technique in the context of studying DNA-protein interactions. © 2017 Elsevier Inc. All rights reserved.

  10. Identification of small-molecule antagonists that inhibit an activator: coactivator interaction.

    Science.gov (United States)

    Best, Jennifer L; Amezcua, Carlos A; Mayr, Bernhard; Flechner, Lawrence; Murawsky, Christopher M; Emerson, Beverly; Zor, Tsaffrir; Gardner, Kevin H; Montminy, Marc

    2004-12-21

    Phosphorylation of the cAMP response element binding protein (CREB) at Ser-133 in response to hormonal stimuli triggers cellular gene expression via the recruitment of the histone acetylase coactivator paralogs CREB binding protein (CBP) and p300 to the promoter. The NMR structure of the CREB:CBP complex, using relevant interaction domains called KID and KIX, respectively, reveals a shallow hydrophobic groove on the surface of KIX that accommodates an amphipathic helix in phospho (Ser-133) KID. Using an NMR-based screening approach on a preselected small-molecule library, we identified several compounds that bind to different surfaces on KIX. One of these, KG-501 (2-naphthol-AS-E-phosphate), targeted a surface distal to the CREB binding groove that includes Arg-600, a residue that is required for the CREB:CBP interaction. When added to live cells, KG-501 disrupted the CREB: CBP complex and attenuated target gene induction in response to cAMP agonist. These results demonstrate the ability of small molecules to interfere with second-messenger signaling cascades by inhibiting specific protein-protein interactions in the nucleus.

  11. Comparison between the classical interaction energy and periodic Hartree-Fock binding energies for the interaction between molecules and surfaces

    International Nuclear Information System (INIS)

    Chacon-Taylor, M.R.; McCarthy, M.I.

    1995-01-01

    The energetics of the H 2 O/MgO(001), HCl/MgO(001), and NH 3 /MgO(001) interface were investigated using the ab initio periodic Hartree-Fock LCAO method and a classical interaction energy model. The QM calculations treated a system that was periodic in two dimensions with the adsorbate approaching a three-layer slab of MgO(001). The authors used an approximation to the classical interaction energy, where the surface is represented by its potential, electric field, and electric field derivatives at the positions of the molecule center of mass, and the molecule is described by its charge, electric dipole, electric quadrupole and polarizability. The potential, electric field and electric field gradient are obtained for the clean three-layer slab using the ab initio periodic Hartree-Fock LCAO method (CRYSTAL) and an optimized split valence basis 8-61G on Mg and 8-51G on O. The charge, electric dipole, and electric quadrupole are calculated using ab initio Hartree-Fock theory (GAUSSIAN-92) with a 6-31G* basis set while the SCF polarizability is determined analytically using the same basis set

  12. 100 years of Einstein's Theory of Brownian Motion: From Pollen ...

    Indian Academy of Sciences (India)

    Debashish Chowdhury. In this part, rotational Brownian motion and. Brownian shape fluctuations of soft materials are discussed. This is followed by an elementary in- troduction to two of the hottest topics in this contemporary area of interdisciplinary research, namely, stochastic resonance and Brownian rat- chet. 1. Beyond ...

  13. Hypertonic saline impedes tumor cell-endothelial cell interaction by reducing adhesion molecule and laminin expression.

    LENUS (Irish Health Repository)

    Shields, Conor J

    2012-02-03

    BACKGROUND: Hypertonic saline infusion dampens inflammatory responses and suppresses neutrophil-endothelial interaction by reducing adhesion molecule expression. This study tested the hypothesis that hypertonic saline attenuates tumor cell adhesion to the endothelium through a similar mechanism. METHODS: Human colon cancer cells (LS174T) were transfected with green fluorescent protein and exposed to lipopolysaccharide, tumor necrosis factor-alpha, and interleukin-6 under hypertonic and isotonic conditions for 1 and 4 hours. Confluent human umbilical vein endothelial cells were similarly exposed. Cellular apoptosis and expression of adhesion molecules and laminin were measured by flow cytometry. Tumor cell adhesion to endothelium and laminin was assessed with fluorescence microscopy. Data are represented as mean +\\/- standard error of mean, and an ANOVA test was performed to gauge statistical significance, with P <.05 considered significant. RESULTS: Hypertonic exposure significantly reduced tumor cell adhesion despite the presence of the perioperative cell stressors (42 +\\/- 2.9 vs 172.5 +\\/- 12.4, P <.05), attenuated tumor cell beta-1 integrin (14.43 vs 23.84, P <.05), and endothelial cell laminin expression (22.78 +\\/- 2.2 vs 33.74 +\\/- 2.4, P <.05), but did not significantly alter cell viability. CONCLUSION: Hypertonic saline significantly attenuates tumor cell adhesion to endothelium by inhibiting adhesion molecule and laminin expression. This may halt the metastatic behavior of tumor cells shed at surgery.

  14. An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles.

    Science.gov (United States)

    Ilie, Ioana M; Briels, Wim J; den Otter, Wouter K

    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.

  15. Small-molecule stabilization of protein-protein interactions: an underestimated concept in drug discovery?

    Science.gov (United States)

    Thiel, Philipp; Kaiser, Markus; Ottmann, Christian

    2012-02-27

    The modulation of protein-protein interactions (PPIs) has been recognized as one of the most challenging tasks in drug discovery. While their systematic development has long been considered as intractable, this view has changed over the last years, with the first drug candidates undergoing clinical studies. To date, the vast majority of PPI modulators are interaction inhibitors. However, in many biological contexts a prolonged lifespan of a PPI might be desirable, calling for the complementary approach of PPI stabilization. In fact, nature offers impressive examples of this concept and some PPI-stabilizing natural products have already found application as important drugs. Moreover, directed small-molecule stabilization has recently been demonstrated. Therefore, it is time to take a closer look at the constructive side of modulating PPIs. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Leishmanolysin-like molecules in Herpetomonas samuelpessoai mediate hydrolysis of protein substrates and interaction with insect.

    Science.gov (United States)

    Pereira, Fernanda M; Dias, Felipe A; Elias, Camila G R; d'Avila-Levy, Claudia M; Silva, Cristina S; Santos-Mallet, Jacenir R; Branquinha, Marta H; Santos, André L S

    2010-10-01

    Herpetomonas samuelpessoai, an insect trypanosomatid, produces a 63-kDa metallopeptidase that has similar biochemical/immunological properties to Leishmania leishmanolysin, a virulence factor that participates in different stages of the parasite life cycle. Herein, we described some biochemical characteristics of the major surface metallopeptidase of H. samuelpessoai that led us to infer some probable functions for this peptidase during the parasite-invertebrate interaction. Gelatin-SDS-PAGE, flow cytometry and confocal fluorescence microscopy provided measurements for the relative levels of surface leishmanolysin-like molecules in H. samuelpessoai. Immunocytochemical analysis demonstrated the presence of leishmanolysin-like molecules on the surface and cytoplasm of the parasite. The surface metallopeptidase was active at a broad spectrum of pH and temperature, showing maximum activity at pH 6.0 at 37 degrees C, and an ability to degrade albumin, hemoglobin, IgG, mucin, casein and gut proteins obtained from Aedes aegypti. This wide substrate utilization might support parasite growth and development. Curiously, H. samuelpessoai cells were able to colonize A. aegypti guts. In an effort to implicate a possible role for the metallopeptidase from H. samuelpessoai, living parasites were treated with different compounds before the interaction with gut cells. The pre-incubation with metallopeptidase inhibitors, phospholipase C or anti-leishmanolysin antibodies promoted a significant reduction in the interaction with guts. Similarly, the pre-treatment of gut cells with purified leishmanolysin-like protein drastically diminished the adhesion process. Furthermore, the expression of surface leishmanolysin in H. samuelpessoai cells was drastically enhanced after passage in A. aegypti. These results suggest the participation of homologues of leishmanolysin in the interaction of H. samuelpessoai with the invertebrate vector. Copyright 2010 Elsevier Ltd. All rights reserved.

  17. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred [Univ. of California, Berkeley, CA (United States)

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  18. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    International Nuclear Information System (INIS)

    Laurence, Ted Alfred

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  19. Generalized Arcsine Laws for Fractional Brownian Motion.

    Science.gov (United States)

    Sadhu, Tridib; Delorme, Mathieu; Wiese, Kay Jörg

    2018-01-26

    The three arcsine laws for Brownian motion are a cornerstone of extreme-value statistics. For a Brownian B_{t} starting from the origin, and evolving during time T, one considers the following three observables: (i) the duration t_{+} the process is positive, (ii) the time t_{last} the process last visits the origin, and (iii) the time t_{max} when it achieves its maximum (or minimum). All three observables have the same cumulative probability distribution expressed as an arcsine function, thus the name arcsine laws. We show how these laws change for fractional Brownian motion X_{t}, a non-Markovian Gaussian process indexed by the Hurst exponent H. It generalizes standard Brownian motion (i.e., H=1/2). We obtain the three probabilities using a perturbative expansion in ϵ=H-1/2. While all three probabilities are different, this distinction can only be made at second order in ϵ. Our results are confirmed to high precision by extensive numerical simulations.

  20. Brownian Motion Problem: Random Walk and Beyond

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 8. Brownian Motion Problem: Random Walk and Beyond. Shama Sharma Vishwamittar. General Article Volume 10 Issue 8 August 2005 pp 49-66. Fulltext. Click here to view fulltext PDF. Permanent link:

  1. 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 ap...

  2. 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.

  3. Temporary Anion States of Ethene Interacting with Single Molecules of Methane, Ethane, and Water.

    Science.gov (United States)

    Sommerfeld, Thomas; Melugin, Joshua B; Ehara, Masahiro

    2018-03-08

    When an excess electron is added into the π* orbital of ethene, the resulting anion decays by electron autodetachment; that is, it represents an electronic state referred to as a temporary anion or resonance state. Here, the influence of a cluster environment on the energy and lifetime of this state is investigated. The clusters considered are ethene···CH 4 , ethene···C 2 H 6 , and ethene···H 2 O. Most of these clusters are systematically constructed so that the solvent interacts with the π system in a specific way, and are thus by construction not minima with respect to all intermolecular degrees of freedom. However, for water, in addition, a minimal energy structure is examined. Systematic variation of the solvent and solvation geometry allows us to identify trends regarding effects due to polarizability, excluded volume, and polarity of the solvent molecules. The resonance parameters of ethene and all temporary cluster anions are computed with the symmetry-adapted cluster-configuration interaction electronic structure method in combination with a complex absorbing potential. This method is well-established for small to intermediate sized molecules. In addition to the study of the solvation effects themselves, the question of how many basis functions are needed on the closed-shell solvating unit is examined.

  4. Plasma-neutral gas interaction in a tokamak divertor: effects of hydrogen molecules and plasma recombination

    International Nuclear Information System (INIS)

    Krasheninnikov, S.I.; Pigarov, A.Yu.; Soboleva, T.K.; Sigmar, D.J.

    1997-01-01

    We investigate the influence of hydrogen molecules on plasma recombination using a collisional-radiative model for multispecies hydrogen plasmas and tokamak detached divertor parameters. The rate constant found for molecular activated recombination of a plasma can be as high as 2 x 10 -10 cm 3 /s, confirming our pervious estimates. We investigate the effects of hydrogen molecules and plasma recombination on self-consistent plasma-neutral gas interactions in the recycling region of a tokamak divertor. We treat the plasma flow in a fluid approximation retaining the effects of plasma recombination and employing a Knudsen neutral transport model for a 'gas box' divertor geometry. For the model of plasma-neutral interactions we employ we find: (a) molecular activated recombination is a dominant channel of divertor plasma recombination; and (b) plasma recombination is a key element leading to a decrease in the plasma flux onto the target and substantial plasma pressure drop which are the main features of detached divertor regimes. (orig.)

  5. Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

    Science.gov (United States)

    Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

    2017-12-01

    Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

  6. Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations

    Science.gov (United States)

    Johnson, David K.; Karanicolas, John

    2015-01-01

    Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings. Structural studies have shown that in many cases, the inhibitor-bound protein adopts a conformation that is distinct from its unbound and its protein-bound conformations. This plasticity of the protein surface presents a major challenge in predicting which members of a protein family will be inhibited by a given ligand. Here, we use biased simulations of Bcl-2-family proteins to generate ensembles of low-energy conformations that contain surface pockets suitable for small molecule binding. We find that the resulting conformational ensembles include surface pockets that mimic those observed in inhibitor-bound crystal structures. Next, we find that the ensembles generated using different members of this protein family are overlapping but distinct, and that the activity of a given compound against a particular family member (ligand selectivity) can be predicted from whether the corresponding ensemble samples a complementary surface pocket. Finally, we find that each ensemble includes certain surface pockets that are not shared by any other family member: while no inhibitors have yet been identified to take advantage of these pockets, we expect that chemical scaffolds complementing these “distinct” pockets will prove highly selective for their targets. The opportunity to achieve target selectivity within a protein family by exploiting differences in surface fluctuations represents a new paradigm that may facilitate design of family-selective small-molecule inhibitors of protein-protein interactions. PMID:25706586

  7. Computer Simulations of Small Molecules in Membranes: Insights from Computer Simulations into the Interactions of Small Molecules with Lipid Bilayers

    Science.gov (United States)

    Pohorille, Andrew; New, Michael H.; Schweighofer, Karl; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    Two of Ernest Overton's lasting contributions to biology are the Meyer-Overton relationship between the potency of an anesthetic and its solubility in oil, and the Overton rule which relates the permeability of a membrane to the oil-water partition coefficient of the permeating molecule. A growing body of experimental evidence, however, cannot be reconciled with these theories. In particular, the molecular nature of membranes, unknown to Overton, needs to be included in any description of these phenomena. Computer simulations are ideally suited for providing atomic-level information about the behavior of small molecules in membranes. The authors discuss simulation studies relevant to Overton's ideas. Through simulations it was found that anesthetics tend to concentrate at interfaces and their anesthetic potency correlates better with solubility at the water-membrane interface than with solubility in oil. Simulation studies of membrane permeation revealed the anisotropic nature of the membranes, as evidenced, for example, by the highly nonuniform distribution of free volume in the bilayer. This, in turn, influences the diffusion rates of solutes, which increase with the depth in the membrane. Small solutes tend to move by hopping between voids in the bilayer, and this hopping motion may be responsible for the deviation from the Overton rule of the permeation rates of these molecules.

  8. Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules.

    Science.gov (United States)

    Janjić, Goran V; Ninković, Dragan B; Zarić, Snezana D

    2013-08-01

    Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

  9. Polarizable charge equilibration model for predicting accurate electrostatic interactions in molecules and solids

    Science.gov (United States)

    Naserifar, Saber; Brooks, Daniel J.; Goddard, William A.; Cvicek, Vaclav

    2017-03-01

    Electrostatic interactions play a critical role in determining the properties, structures, and dynamics of chemical, biochemical, and material systems. These interactions are described well at the level of quantum mechanics (QM) but not so well for the various models used in force field simulations of these systems. We propose and validate a new general methodology, denoted PQEq, to predict rapidly and dynamically the atomic charges and polarization underlying the electrostatic interactions. Here the polarization is described using an atomic sized Gaussian shaped electron density that can polarize away from the core in response to internal and external electric fields, while at the same time adjusting the charge on each core (described as a Gaussian function) so as to achieve a constant chemical potential across all atoms of the system. The parameters for PQEq are derived from experimental atomic properties of all elements up to Nobelium (atomic no. = 102). We validate PQEq by comparing to QM interaction energy as probe dipoles are brought along various directions up to 30 molecules containing H, C, N, O, F, Si, P, S, and Cl atoms. We find that PQEq predicts interaction energies in excellent agreement with QM, much better than other common charge models such as obtained from QM using Mulliken or ESP charges and those from standard force fields (OPLS and AMBER). Since PQEq increases the accuracy of electrostatic interactions and the response to external electric fields, we expect that PQEq will be useful for a large range of applications including ligand docking to proteins, catalytic reactions, electrocatalysis, ferroelectrics, and growth of ceramics and films, where it could be incorporated into standard force fields as OPLS, AMBER, CHARMM, Dreiding, ReaxFF, and UFF.

  10. Interaction of von Willebrand factor domains with collagen investigated by single molecule force spectroscopy

    Science.gov (United States)

    Posch, Sandra; Obser, Tobias; König, Gesa; Schneppenheim, Reinhard; Tampé, Robert; Hinterdorfer, Peter

    2018-03-01

    von Willebrand factor (VWF) is a huge multimeric protein that plays a key role in primary hemostasis. Sites for collagen binding, an initial event of hemostasis, are located in the VWF-domains A1 and A3. In this study, we investigated single molecule interactions between collagen surfaces and wild type VWF A1A2A3 domain constructs, as well as clinically relevant VWF A3 domain point mutations, such as p.Ser1731Thr, p.Gln1734His, and p.His1786Arg. For this, we utilized atomic force microscopy based single molecular force spectroscopy. The p.Ser1731Thr mutant had no impact on the VWF-collagen type III and VI interactions, while the p.Gln1734His and p.His1786Arg mutants showed a slight increase in bond stability to collagen type III. This effect probably arises from additional hydrogen bonds that come along with the introduction of these mutations. Using the same mutants, but collagen type VI as a binding partner, resulted in a significant increase in bond stability. VWF domain A1 was reported to be essential for the interaction with collagen type VI and thus our findings strengthen the hypothesis that the VWF A1 domain can compensate for mutations in the VWF A3 domain. Additionally, our data suggest that the mutations could even stabilize the interaction between VWF and collagen without shear. VWF-collagen interactions seem to be an important system in which defective interactions between one VWF domain and one type of collagen can be compensated by alternative binding events.

  11. Phospholipid monolayer coated microfabricated electrodes to model the interaction of molecules with biomembranes

    Energy Technology Data Exchange (ETDEWEB)

    Coldrick, Zachary [Centre for Self-Organising Molecular Systems (SOMS), School of Chemistry, University of Leeds, Leeds, LS2 9JT (United Kingdom)], E-mail: eenzc@leeds.ac.uk; Steenson, Paul [School of Electronic Engineering, University of Leeds, Leeds, LS2 9JT (United Kingdom); Millner, Paul [Institute of Membrane and Systems Biology, University of Leeds, Leeds, LS2 9JT (United Kingdom); Davies, Matthew [Health and Safety Laboratories, Buxton, SK17 9JN (United Kingdom); Nelson, Andrew [Centre for Self-Organising Molecular Systems (SOMS), School of Chemistry, University of Leeds, Leeds, LS2 9JT (United Kingdom)

    2009-09-01

    The hanging mercury (Hg) drop electrode (HMDE) has a classical application as a tool to study adsorption and desorption processes of surface organic films due to its: (a) atomically smooth surface and, (b) hydrophobicity at its potential of zero charge. In this study we report on a replacement of the HMDE for studying supported organic layers in the form of platinum (Pt) working electrodes fabricated using lithography techniques on which a thin film of Hg is electrodeposited. These wafer-based Pt/Hg electrodes are characterised and compared to the HMDE using rapid cyclic voltammetry (RCV) and show similar capacitance-potential profiles while being far more mechanically stable and consuming considerably less Hg over their lifetime of several months. The electrodes have been used to support self-assembled phospholipid monolayers which are dynamic surface coatings with unique dielectric properties. The issue of surface contamination has been solved by regenerating the electrode surface prior to phospholipid coating by application of extreme cathodic potentials more negative than -2.6 V (vs. Ag/AgCl). The phospholipid coated electrodes presented in this paper mimic one half of a phospholipid bilayer and exhibit interactions with the biomembrane active drug molecules chlorpromazine, and quinidine. The magnitudes of these interactions have been assessed by recording changes in the capacitance-potential profiles in real time using RCV at 40 V s{sup -1} over potential ranges >1 V. A method for electrode coating with phospholipids with the electrodes fitted in a flow cell device has been developed. This has enabled sequential rapid cleaning/coating/interaction cycles for the purposes of drug screening and/or on-line monitoring for molecules of interest.

  12. Phospholipid monolayer coated microfabricated electrodes to model the interaction of molecules with biomembranes

    International Nuclear Information System (INIS)

    Coldrick, Zachary; Steenson, Paul; Millner, Paul; Davies, Matthew; Nelson, Andrew

    2009-01-01

    The hanging mercury (Hg) drop electrode (HMDE) has a classical application as a tool to study adsorption and desorption processes of surface organic films due to its: (a) atomically smooth surface and, (b) hydrophobicity at its potential of zero charge. In this study we report on a replacement of the HMDE for studying supported organic layers in the form of platinum (Pt) working electrodes fabricated using lithography techniques on which a thin film of Hg is electrodeposited. These wafer-based Pt/Hg electrodes are characterised and compared to the HMDE using rapid cyclic voltammetry (RCV) and show similar capacitance-potential profiles while being far more mechanically stable and consuming considerably less Hg over their lifetime of several months. The electrodes have been used to support self-assembled phospholipid monolayers which are dynamic surface coatings with unique dielectric properties. The issue of surface contamination has been solved by regenerating the electrode surface prior to phospholipid coating by application of extreme cathodic potentials more negative than -2.6 V (vs. Ag/AgCl). The phospholipid coated electrodes presented in this paper mimic one half of a phospholipid bilayer and exhibit interactions with the biomembrane active drug molecules chlorpromazine, and quinidine. The magnitudes of these interactions have been assessed by recording changes in the capacitance-potential profiles in real time using RCV at 40 V s -1 over potential ranges >1 V. A method for electrode coating with phospholipids with the electrodes fitted in a flow cell device has been developed. This has enabled sequential rapid cleaning/coating/interaction cycles for the purposes of drug screening and/or on-line monitoring for molecules of interest.

  13. Investigation of the Hydantoin Monomer and its Interaction with Water Molecules

    Science.gov (United States)

    Gruet, Sébastien; Perez, Cristobal; Schnell, Melanie

    2017-06-01

    Hydantoin (Imidazolidine-2,4-dione, C_3H_4N_2O_2) is a five-membered heterocyclic compound of astrobiological interest. This molecule has been detected in carbonaceous chondrites [1], and its formation can rise from the presence of glycolic acid and urea, two prebiotic molecules [2]. The hydrolysis of hydantoin under acidic conditions can also produce glycine [3], an amino acid actively searched for in the interstellar medium. Spectroscopic data of hydantoin is very limited and mostly dedicated to the solid phase. The high resolution study in gas phase is restricted to the work recently published by Ozeki et al. reporting the pure rotational spectra of the ground state and two vibrational states of the molecule in the millimeter-wave region (90-370 GHz)[4]. Using chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy, we recorded the jet-cooled rotational spectra of hydantoin with water between 2 to 8 GHz. We observed the ground state of hydantoin monomer and several water complexes with one or two water molecules. All the observed species exhibit a hyperfine structure due to the two nitrogen atoms present in the molecule, which were fully resolved and analyzed. Additional experiments with a ^{18}O enriched water sample were realized to determine the oxygen-atom positions of the water monomers. These experiments yielded accurate structural information on the preferred water binding sites. The observed complexes and the interactions that hold them together, mainly strong directional hydrogen bonds, will be presented and discussed. [1] Shimoyama, A. and Ogasawara, R., Orig. Life Evol. Biosph., 32, 165-179, 2002. DOI:10.1023/A:1016015319112. [2] Menor-Salván, C. and Marín-Yaseli, M.R., Chem. Soc. Rev., 41(16), 5404-5415, 2012. DOI:10.1039/c2cs35060b. [3] De Marcellus P., Bertrand M., Nuevo M., Westall F. and Le Sergeant d'Hendecourt L., Astrobiology. 11(9), 847-854, 2011. DOI:10.1089/ast.2011.0677. [4] Ozeki, H., Miyahara R., Ihara H., Todaka S., Kobayashi

  14. [Functional analysis of cancer-derived immunoglobulin G whole molecule-interacting proteins identified by LC-MS/MS].

    Science.gov (United States)

    Wang, Ju-Ping; Chen, Han-Ying; Peng, Hui

    2015-01-01

    To identify cancer-derived immunoglobulin G (IgG) whole molecule-interacting proteins to provide important clues for studying IgG biological functions. HeLa cell lysate was immunoprecipitated with rabbit antihuman IgG whole molecule antibody and normal rabbit IgG. The immunocomplex underwent sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and was detected with silver staining. Three prominently enhanced bands were subjected to protein identification with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the MS data were analyzed with Swiss-Prot database. Cancer-derived IgG whole molecule-interacting proteins were screened and functionally annotated. We identified 6 potential cancer-derived IgG whole molecule-interacting proteins with co-immunoprecipitation combined with LC-MS/MS, which provides valuable clues for studying the function of cancer-derived IgG.

  15. How to Measure Load-Dependent Kinetics of Individual Motor Molecules Without a Force-Clamp

    DEFF Research Database (Denmark)

    Sung, Jongmin; Mortensen, Kim; Spudich, James A.

    Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using a new method, Harmonic Force...... and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human beta-cardiac myosin molecules interacting with an actin filament...... at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load. This points to Kramer's Brownian diffusion model of chemical reactions as explanation why muscle contracts with a velocity inversely proportional to external load....

  16. Revealing Two-State Protein-Protein Interaction of Calmodulin by Single-Molecule Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ruchuan; Hu, Dehong; Tan, Xin; Lu, H PETER.

    2006-08-09

    We report a single-molecule fluorescence resonance energy transfer (FRET) and polarization study of conformational dynamics of calmodulin (CaM) interacting with a target peptide, C28W of 28 amino-acid oligomer. The C28W peptide represents the essential binding sequence domain of the Ca-ATPase protein interacting with CaM, which is important in cellular signaling for the regulation of energy in metabolism. However, the mechanism of the CaM-C28W recognition complex formation is still unclear. The amino-terminal (N-terminal) domain of the CaM was labeled with a fluorescein-based arsenical hairpin binder (F1AsH) that enables our unambiguously probing the CaM N-terminal target-binding domain motions at a millisecond timescale without convolution of the probe-dye random motions. By analyzing the distribution of FRET efficiency between F1AsH labeled CaM and Texas Red labeled C28W and the polarization fluctuation dynamics and distributions of the CaM N-terminal domain, we reveal slow (at sub-second time scale) binding-unbinding motions of the N-terminal domain of the CaM in CaM-C28W complexes, which is a strong evidence of a two-state binding interaction of CaM-mediated cell signaling.

  17. Distance-dependent interactions between gold nanoparticles and fluorescent molecules with DNA as tunable spacers

    International Nuclear Information System (INIS)

    Chhabra, Rahul; Sharma, Jaswinder; Lin Su; Yan Hao; Lindsay, Stuart; Liu Yan; Wang Haining; Zou Shengli

    2009-01-01

    Using stoichiometrically controlled 1:1 functionalization of gold nanoparticles with fluorescent dye molecules in which the dye molecule is held away from the particle surface by a rigid DNA spacer allows precise determination of the distance-dependent effect of the metal nanoparticles on fluorescence intensity. Two dyes were studied, Cy3 and Cy5, with two sizes of nanoparticles, 5 and 10 nm. The larger the particle, the more quenching of the photoluminescence (PL) intensity, due to increased overlap of the dye's emission spectrum with the Au surface plasmon resonance. Fluorescence is quenched significantly for distances somewhat larger than the particle diameter, in good agreement with the predictions of an electrodynamics model based on interacting dipoles. The distance dependence of surface energy transfer behavior, i.e. quenching efficiency, is proportional to 1/d 4 , which involves no consideration of the size of the particle and the spectral overlap of the dye and AuNp. This surface energy transfer model is found qualitatively and agrees with the electrodynamic model, though the exponent is greater than 4 for the smaller nanoparticles (5 nm), and smaller than 4 for the larger nanoparticles (10 nm).

  18. Distance-dependent interactions between gold nanoparticles and fluorescent molecules with DNA as tunable spacers

    Energy Technology Data Exchange (ETDEWEB)

    Chhabra, Rahul; Sharma, Jaswinder; Lin Su; Yan Hao; Lindsay, Stuart; Liu Yan [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Wang Haining; Zou Shengli, E-mail: stuart.lindsay@asu.ed, E-mail: yan_liu@asu.ed [Department of Chemistry, University of Central Florida, Orlando, FL 32816 (United States)

    2009-12-02

    Using stoichiometrically controlled 1:1 functionalization of gold nanoparticles with fluorescent dye molecules in which the dye molecule is held away from the particle surface by a rigid DNA spacer allows precise determination of the distance-dependent effect of the metal nanoparticles on fluorescence intensity. Two dyes were studied, Cy3 and Cy5, with two sizes of nanoparticles, 5 and 10 nm. The larger the particle, the more quenching of the photoluminescence (PL) intensity, due to increased overlap of the dye's emission spectrum with the Au surface plasmon resonance. Fluorescence is quenched significantly for distances somewhat larger than the particle diameter, in good agreement with the predictions of an electrodynamics model based on interacting dipoles. The distance dependence of surface energy transfer behavior, i.e. quenching efficiency, is proportional to 1/d{sup 4}, which involves no consideration of the size of the particle and the spectral overlap of the dye and AuNp. This surface energy transfer model is found qualitatively and agrees with the electrodynamic model, though the exponent is greater than 4 for the smaller nanoparticles (5 nm), and smaller than 4 for the larger nanoparticles (10 nm).

  19. A Synthetic Biology Project - Developing a single-molecule device for screening drug-target interactions.

    Science.gov (United States)

    Firman, Keith; Evans, Luke; Youell, James

    2012-07-16

    This review describes a European-funded project in the area of Synthetic Biology. The project seeks to demonstrate the application of engineering techniques and methodologies to the design and construction of a biosensor for detecting drug-target interactions at the single-molecule level. Production of the proteins required for the system followed the principle of previously described "bioparts" concepts (a system where a database of biological parts - promoters, genes, terminators, linking tags and cleavage sequences - is used to construct novel gene assemblies) and cassette-type assembly of gene expression systems (the concept of linking different "bioparts" to produce functional "cassettes"), but problems were quickly identified with these approaches. DNA substrates for the device were also constructed using a cassette-system. Finally, micro-engineering was used to build a magnetoresistive Magnetic Tweezer device for detection of single molecule DNA modifying enzymes (motors), while the possibility of constructing a Hall Effect version of this device was explored. The device is currently being used to study helicases from Plasmodium as potential targets for anti-malarial drugs, but we also suggest other potential uses for the device. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  20. Small-Molecule Stabilization of 14-3-3 Protein-Protein Interactions Stimulates Axon Regeneration.

    Science.gov (United States)

    Kaplan, Andrew; Morquette, Barbara; Kroner, Antje; Leong, SooYuen; Madwar, Carolin; Sanz, Ricardo; Banerjee, Sara L; Antel, Jack; Bisson, Nicolas; David, Samuel; Fournier, Alyson E

    2017-03-08

    Damaged central nervous system (CNS) neurons have a poor ability to spontaneously regenerate, causing persistent functional deficits after injury. Therapies that stimulate axon growth are needed to repair CNS damage. 14-3-3 adaptors are hub proteins that are attractive targets to manipulate cell signaling. We identify a positive role for 14-3-3s in axon growth and uncover a developmental regulation of the phosphorylation and function of 14-3-3s. We show that fusicoccin-A (FC-A), a small-molecule stabilizer of 14-3-3 protein-protein interactions, stimulates axon growth in vitro and regeneration in vivo. We show that FC-A stabilizes a complex between 14-3-3 and the stress response regulator GCN1, inducing GCN1 turnover and neurite outgrowth. These findings show that 14-3-3 adaptor protein complexes are druggable targets and identify a new class of small molecules that may be further optimized for the repair of CNS damage. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Direct measurement of interaction forces between a platinum dichloride complex and DNA molecules.

    Science.gov (United States)

    Muramatsu, Hiroshi; Shimada, Shogo; Okada, Tomoko

    2017-09-01

    The interaction forces between a platinum dichloride complex and DNA molecules have been studied using atomic force microscopy (AFM). The platinum dichloride complex, di-dimethylsulfoxide-dichloroplatinum (II) (Pt(DMSO) 2 Cl 2 ), was immobilized on an AFM probe by coordinating the platinum to two amino groups to form a complex similar to Pt(en)Cl 2 , which is structurally similar to cisplatin. The retraction forces were measured between the platinum complex and DNA molecules immobilized on mica plates using force curve measurements. The histogram of the retraction force for λ-DNA showed several peaks; the unit retraction force was estimated to be 130 pN for a pulling rate of 60 nm/s. The retraction forces were also measured separately for four single-base DNA oligomers (adenine, guanine, thymine, and cytosine). Retraction forces were frequently observed in the force curves for the DNA oligomers of guanine and adenine. For the guanine DNA oligomer, the most frequent retraction force was slightly lower than but very similar to the retraction force for λ-DNA. A higher retraction force was obtained for the adenine DNA oligomer than for the guanine oligomer. This result is consistent with a higher retraction activation energy of adenine with the Pt complex being than that of guanine because the kinetic rate constant for retraction correlates to exp(FΔx - ΔE) where ΔE is an activation energy, F is an applied force, and Δx is a displacement of distance.

  2. Interaction of epitaxial silicene with overlayers formed by exposure to Al atoms and O2 molecules.

    Science.gov (United States)

    Friedlein, R; Van Bui, H; Wiggers, F B; Yamada-Takamura, Y; Kovalgin, A Y; de Jong, M P

    2014-05-28

    As silicene is not chemically inert, the study and exploitation of its electronic properties outside of ultrahigh vacuum environments require the use of insulating capping layers. In order to understand if aluminum oxide might be a suitable encapsulation material, we used high-resolution synchrotron photoelectron spectroscopy to study the interactions of Al atoms and O2 molecules, as well as the combination of both, with epitaxial silicene on thin ZrB2(0001) films grown on Si(111). The deposition of Al atoms onto silicene, up to the coverage of about 0.4 Al per Si atoms, has little effect on the chemical state of the Si atoms. The silicene-terminated surface is also hardly affected by exposure to O2 gas, up to a dose of 4500 L. In contrast, when Al-covered silicene is exposed to the same dose, a large fraction of the Si atoms becomes oxidized. This is attributed to dissociative chemisorption of O2 molecules by Al atoms at the surface, producing reactive atomic oxygen species that cause the oxidation. It is concluded that aluminum oxide overlayers prepared in this fashion are not suitable for encapsulation since they do not prevent but actually enhance the degradation of silicene.

  3. Quantitative Analysis of the Interaction Strength and Dynamics of Human IgG4 Half Molecules by Native Mass Spectrometry

    NARCIS (Netherlands)

    Rose, Rebecca J.; Labrijn, Aran F.; van den Bremer, Ewald T. J.; Loverix, Stefan; Lasters, Ignace; van Berkel, Patrick H. C.; van de Winkel, Jan G. J.; Schuurman, Janine; Parren, Paul W. H. I.; Heck, Albert J. R.

    2011-01-01

    Native mass spectrometry (MS) is a powerful technique for studying noncovalent protein-protein interactions. Here, native MS was employed to examine the noncovalent interactions involved in homodimerization of antibody half molecules (HL) in hinge-deleted human IgG4 (IgG4 Delta hinge). By analyzing

  4. To bend or not to bend – are heteroatom interactions within conjugated molecules effective in dictating conformation and planarity?

    KAUST Repository

    Conboy, Gary

    2016-04-26

    We consider the roles of heteroatoms (mainly nitrogen, the halogens and the chalcogens) in dictating the conformation of linear conjugated molecules and polymers through non-covalent intramolecular interactions. Whilst hydrogen bonding is a competitive and sometimes more influential interaction, we provide unambiguous evidence that heteroatoms are able to determine the conformation of such materials with reasonable predictability.

  5. The impact of coulombic interactions among polar molecules and metal substrates on flow and lubrication properties

    Science.gov (United States)

    Gkagkas, K.; Ponnuchamy, V.

    2017-09-01

    In the current work we present an extensive study on the impact of short- and long-range interactions between solids and liquids on the hydrodynamic and lubrication behaviour of a tribological system. We have implemented a coarse grain molecular dynamics description of two ionic liquids (ILs) as lubricants which are confined by two infinitely long flat iron solids and which are subjected to a shearing flow. The impact of surface polarizability and molecule geometry on the ion arrangement under shearing has been studied in detail. The results have revealed two regimes of lubrication, with a liquid phase being present under low normal loads, while solidification of the ILs, accompanied by a steep rise of normal forces and significant wall slip is observed at small plate-to-plate distances.

  6. Triple Effect of Mimetic Peptides Interfering with Neural Cell Adhesion Molecule Homophilic Cis Interactions

    DEFF Research Database (Denmark)

    Li, S. Z.; Kolkova, Kateryna; Rudenko, Olga

    2005-01-01

    on neurite extension and adhesion. To evaluate how interference of these mimetic peptides with NCAM homophilic interactions in cis influences NCAM binding in trans, we employed a coculture system in which PC12-E2 cells were grown on monolayers of fibroblasts with or without NCAM expression and the rate...... of neurite outgrowth subsequently was analyzed. P2, but not P1-B, induced neurite outgrowth in the absence of NCAM binding in trans. When PC12-E2 cells were grown on monolayers of NCAM-expressing fibroblasts, the effect of both P1-B and P2 on neurite outgrowth was dependent on peptide concentrations. P1-B......The neural cell adhesion molecule (NCAM) is pivotal in neural development, regeneration, and learning. Here we characterize two peptides, termed P1-B and P2, derived from the homophilic binding sites in the first two N-terminal immunoglobulin (Ig) modules of NCAM, with regard to their effects...

  7. Rovibrational interaction and vibrational constants of the symmetric top molecule 14NF3.

    Science.gov (United States)

    Najib, Hamid

    2013-01-01

    Several accurate experimental values of the α(C) and α(B) rotation-vibration interaction parameters and ω(i), x(ij), and g(ij) vibrational constants have been extracted from the most recent high-resolution Fourier transform infrared, millimeter wave, and centimeter wave investigations in the spectra of the oblate symmetric top molecule (14)NF3. The band-centres used are those of the four fundamental, the overtones, the combination, and hot bands identified in the region between 400 cm(-1) and 2000 cm(-1). Comparison of our constants with the ones measured previously, by infrared spectroscopy at low resolution, reveals orders of magnitude higher accuracy of the new values. The agreement between our values and those determined by ab initio calculations employing the TZ2Pf basis is excellent.

  8. Rovibrational Interaction and Vibrational Constants of the Symmetric Top Molecule 14NF3

    Directory of Open Access Journals (Sweden)

    Hamid Najib

    2013-01-01

    Full Text Available Several accurate experimental values of the and rotation-vibration interaction parameters and , , and vibrational constants have been extracted from the most recent high-resolution Fourier transform infrared, millimeter wave, and centimeter wave investigations in the spectra of the oblate symmetric top molecule 14NF3. The band-centres used are those of the four fundamental, the overtones, the combination, and hot bands identified in the region between 400 cm−1 and 2000 cm−1. Comparison of our constants with the ones measured previously, by infrared spectroscopy at low resolution, reveals orders of magnitude higher accuracy of the new values. The agreement between our values and those determined by ab initio calculations employing the TZ2Pf basis is excellent.

  9. Fractional Brownian motion with a reflecting wall

    Science.gov (United States)

    Wada, Alexander H. O.; Vojta, Thomas

    2018-02-01

    Fractional Brownian motion, a stochastic process with long-time correlations between its increments, is a prototypical model for anomalous diffusion. We analyze fractional Brownian motion in the presence of a reflecting wall by means of Monte Carlo simulations. Whereas the mean-square displacement of the particle shows the expected anomalous diffusion behavior ˜tα , the interplay between the geometric confinement and the long-time memory leads to a highly non-Gaussian probability density function with a power-law singularity at the barrier. In the superdiffusive case α >1 , the particles accumulate at the barrier leading to a divergence of the probability density. For subdiffusion α <1 , in contrast, the probability density is depleted close to the barrier. We discuss implications of these findings, in particular, for applications that are dominated by rare events.

  10. Brownian motion, martingales, and stochastic calculus

    CERN Document Server

    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...

  11. Detrended Fluctuation Analysis of multifractional Brownian motion

    Science.gov (United States)

    Setty, Venkat; Sharma, Surjalal

    2013-03-01

    Multifractional Brownian Motion (mBm) is a generalization of Fractional Brownian motion (fBm) with a time varying Hurst exponent, H (t) . Detrended Fluctuation Analysis (DFA) is a technique used to study the scaling behavior representing long term correlations in various dynamical systems. In our work, we apply DFA to calculate a time averaged Hurst exponent, in mBm data. The accuracy of estimation of was shown to depend on the range and variability of H (t) . Furthermore, the effect of uniform random noise in H (t) on the nature of scaling observed in DFA is studied. Our research focusses on the robustness and applicability of the DFA technique for studying long term correlations in systems with time varying Hurst exponents akin to mBm .

  12. Velocity Gradient Power Functional for Brownian Dynamics

    Science.gov (United States)

    de las Heras, Daniel; Schmidt, Matthias

    2018-01-01

    We present an explicit and simple approximation for the superadiabatic excess (over ideal gas) free power functional, admitting the study of the nonequilibrium dynamics of overdamped Brownian many-body systems. The functional depends on the local velocity gradient and is systematically obtained from treating the microscopic stress distribution as a conjugate field. The resulting superadiabatic forces are beyond dynamical density functional theory and are of a viscous nature. Their high accuracy is demonstrated by comparison to simulation results.

  13. The quantum brownian particle and memory effects

    International Nuclear Information System (INIS)

    Britani, J.R.; Mizrahi, S.S.; Pimentel, B.M.

    1991-01-01

    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)

  14. Time-averaged MSD of Brownian motion

    OpenAIRE

    Andreanov, Alexei; Grebenkov, Denis

    2012-01-01

    We study the statistical properties of the time-averaged mean-square displacements (TAMSD). This is a standard non-local quadratic functional for inferring the diffusion coefficient from an individual random trajectory of a diffusing tracer in single-particle tracking experiments. For Brownian motion, we derive an exact formula for the Laplace transform of the probability density of the TAMSD by mapping the original problem onto chains of coupled harmonic oscillators. From this formula, we de...

  15. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    Science.gov (United States)

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  16. Intense Interactions of Molecules with a Short-Wavelength Electromagnetic Radiation Field: I. The Fundamentals of the Nonadiabatic Theory

    Science.gov (United States)

    Pegarkov, A. I.

    2001-07-01

    The intense interactions between short-wavelength (SW) electromagnetic radiation with a wavelength λ ≥ 1 Å and intensity up to 1014 W/cm2 and simple and polyatomic molecules are studied with the coherent excitations of high-lying Rydberg and autoionizing states taken into account. The Hamiltonian of a system "molecule + SW radiation" is obtained by using the methods of quantum electrodynamics. Conditions for the applicability of the dipole approximation to describe the interactions of molecules with radiation of the UV, VUV, XUV, and soft X-ray range are found. The fundamentals of the theory of resonance scattering of SW radiation from diatomic, triatomic, and symmetric-and asymmetric-top polyatomic molecules are outlined.

  17. Physical manipulation of single-molecule DNA using microbead and its application to analysis of DNA-protein interaction

    International Nuclear Information System (INIS)

    Kurita, Hirofumi; Yasuda, Hachiro; Takashima, Kazunori; Katsura, Shinji; Mizuno, Akira

    2009-01-01

    We carried out an individual DNA manipulation using an optical trapping for a microbead. This manipulation system is based on a fluorescent microscopy equipped with an IR laser. Both ends of linear DNA molecule were labeled with a biotin and a thiol group, respectively. Then the biotinylated end was attached to a microbead, and the other was immobilized on a thiol-linkable glass surface. We controlled the form of an individual DNA molecule by moving the focal point of IR laser, which trapped the microbead. In addition, we applied single-molecule approach to analyze DNA hydrolysis. We also used microchannel for single-molecule observation of DNA hydrolysis. The shortening of DNA in length caused by enzymatic hydrolysis was observed in real-time. The single-molecule DNA manipulation should contribute to elucidate detailed mechanisms of DNA-protein interactions

  18. Dynamics of Brownian motors in deformable medium

    Science.gov (United States)

    Woulaché, Rosalie Laure; Kepnang Pebeu, Fabrice Maxime; Kofané, Timoléon C.

    2016-10-01

    The directed transport in a one-dimensional overdamped, Brownian motor subjected to a travelling wave potential with variable shape and exposed to an external bias is studied numerically. We focus our attention on the class of Remoissenet-Peyrard parametrized on-site potentials with slight modification, whose shape can be varied as a function of a parameter s, recovering the sine-Gordon shape as the special case. We demonstrate that in the presence of the travelling wave potential the observed dynamical properties of the Brownian motor which crucially depends on the travelling wave speed, the intensity of the noise and the external load is significantly influenced also by the geometry of the system. In particular, we notice that systems with sharp wells and broad barriers favour the transport under the influence of an applied load. The efficiency of transport of Brownian motors in deformable systems remains equal to 1 (in the absence of an applied load) up to a critical value of the travelling wave speed greater than that of the pure sine-Gordon shape.

  19. Third version of a program for calculating the static interaction potential between an electron and a diatomic molecule

    International Nuclear Information System (INIS)

    Raseev, G.

    1980-01-01

    This program calculates the one-centre expansion of a two-centre wave function of a diatomic molecule and also the multipole expansion of its static interaction with a point charge. It is an extension to some classes of open-shell targets of the previous versions and it provides both the wave function and the potential in a form suitable for use in an electron-molecule scattering program. (orig./HSI)

  20. Effect of Dipolar Interactions on the Magnetization of Single-Molecule Magnets in a cubic lattice

    Science.gov (United States)

    Alcantara Ortigoza, Marisol

    2005-03-01

    Since the one-body tunnel picture of single-molecule magnets (SMM) is not always sufficient to explain the fine structure of experimental hysteresis loops, the effect of intermolecular dipolar interactions has been investigated on an ensemble of 100 3D-systems of 5X5X4 particles, each with spin S = 5, arranged in a cubic lattice. We have solved the Landau-Lifshitz-Gilbert equation for several values of the damping constant, the field sweep rate and the lattice constant. We find that the smaller the damping constant is, the stronger the maximum field needs to be to produce hysteresis. Furthermore, the shape of the hysteresis loops also depends on the damping constant. We also find that the system magnetizes and demagnetizes faster with decreasing sweep rates, resulting in smaller hysteresis loops. Variations of the lattice constant within realistic values (1.5nm and 2.5nm) show that the dipolar interaction plays an important role in magnetic hysteresis by controlling the relaxation process. Examination of temperature dependencies (0.1K and 0.7K) of the above will be presented and compared with recent experimental data on SMM.

  1. [Impact of stromal interaction molecule 1 silencing on cell cycle of endothelial progenitor cells].

    Science.gov (United States)

    Kuang, Chun-Yan; Huang, Lan; Yu, Yang; Deng, Meng-Yang; Wang, Kui; Qian, De-Hui

    2011-07-01

    To investigate the effect of stromal interaction molecule 1 (STIM1) silencing on EPCs cell cycle. Rat bone marrow derived endothelial progenitor cells (EPCs) were isolated and cultured in L-DMEM with 20% FBS. Ad-si/rSTIM1 and Ad-hSTIM1 were then transfected into EPCs and the expression of STIM1 mRNA was detected by RT-PCR. The cell cycle was determined using flow cytometry analysis and intracellular free Ca2+ was measured using LSCM. Co-immunoprecipitation was performed to examine the interaction between STIM1 and TRPC1. Protein levels of inositol 1, 4, 5-trisphosphate were analyzed with ELISA assay. Forty-eight hours after transfection, the expression of STIM1 mRNA was significantly downregulated (0.37 +/- 0.02 vs. 1.00 +/- 0.02, P si/rSTIM1 group compared with control group. The cell cycle was arrested at G1 phase [(90.91 +/- 1.10)% vs. (77.10 +/- 0.56)%, P si/rSTIM1. However, cotransfection of Ad-hSTIM1 with Ad-si/rSTIM1 significantly reversed these responses. Interestingly, co-immunoprecipitation study showed that STIM1 co-precipitated with TRPC1, and IP3 levels measured by ELISA were similar among three groups (P > 0.05). siRNA-mediated knockdown of STIM1 inhibited EPCs proliferation by reducing intracellular free Ca2+ through TRPC1-SOC signaling pathway.

  2. Extracellular Protein Interactions Mediated by the Neural Cell Adhesion Molecule, NCAM: Heterophilic Interactions Between NCAM and Cell Adhesion Molecules, Extracellular Matrix Proteins, and Viruses

    DEFF Research Database (Denmark)

    Nielsen, Janne; Kulahin, Nikolaj; Walmod, Peter

    2008-01-01

    interactions, thereby modulating a range of biological processes. This review summarizes interactions between NCAM and other CAMs and ECM proteins. Additionally, the role of NCAM as a receptor for rabies virus, and its implications in rabies infections is briefly described. Interactions between NCAM and its...

  3. A new look on the formation and interaction of elementary particles in atoms and molecules including photoreaction centers.

    Science.gov (United States)

    Shuvalov, V A

    2008-01-01

    Possible role of high-energy bosons (virtual photons) is discussed with respect to the formation of elementary particles and their interaction in nucleus, many-electron atom, and molecule including photoreaction centers. Using properties of the photons, the expressions for calculations of the mass of particles, of the energy of electrons and their distances from nucleus in atoms, of the dissociation energy and distances between atoms in molecules were found which give results in good agreement with experimental data. This approach allows doing calculations in rather complicated system like photoreaction centers in which chlorophyll molecules form electron transfer chain.

  4. Role of high-order dispersion on strong-field laser-molecule interactions

    Science.gov (United States)

    Dantus, Marcos; Nairat, Muath

    2016-05-01

    Strong-field (1012- 1016 W/ cm2) laser-matter interactions are characterized by the extent of fragmentation and charge of the resulting ions as a function of peak intensity and pulse duration. Interactions are influenced by high-order dispersion, which is difficult to characterize and compress. Fourth-order dispersion (FOD) causes a time-symmetric pedestal, while third-order dispersion (TOD) causes a leading (negative) or following (positive) pedestal. Here, we report on strong-field interactions with pentane and toluene molecules, tracking the molecular ion and the doubly charged carbon ion C2+ yields as a function of TOD and FOD for otherwise transform-limited (TL) 35fs pulses. We find TL pulses enhance molecular ion yield and suppress C2+ yield, while FOD reverses this trend. Interestingly, the leading pedestal in negative TOD enhances C2+ yield compared to positive TOD. Pulse pedestals are of particular importance in strong-field science because target ionization or alignment can be induced well before the main pulse arrives. A pedestal following an intense laser pulse can cause sequential ionization or accelerate electrons causing cascaded ionization. Control of high-order dispersion allows us to provide strong-field measurements that can help address the mechanisms responsible for different product ions in the presence and absence of pedestals. Financial support of this work comes from the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy, DOE SISGR (DE-SC0002325)

  5. Geometry of simple molecules: nonbonded interactions, not bonding orbitals, and primarily determine observed geometries.

    Science.gov (United States)

    See, R F; Dutoi, A D; McConnell, K W; Naylor, R M

    2001-03-28

    The forces responsible for the observed geometries of the YX(3) (Y = N or P; X = H, F, or Cl) molecules were studied through ab initio computations at the HF-SCF/6-31G level. The calculated molecular orbitals were grouped as contributing primarily to (a) the covalent bonds, (b) the terminal atom nonbonding electrons (for X = F or Cl), and (c) the central atom nonbonding electrons. This grouping was accomplished through 3-D plotting and an atomic population analysis of the molecular orbitals. The molecules were then moved through a X-Y-X angular range from 90 degrees to 119 degrees, in four or five degree increments. Single-point calculations were done at each increment, so as to quantify the energy changes in the molecular orbital groups as a function of geometry. These calculations show that the nonbonding electrons are much more sensitive to geometry change than are the bonding orbitals, particularly in the trihalide compounds. The molecular orbitals representing the nonbonding electrons on the terminal atoms (both valence and core electrons) contribute to the spreading forces, as they favor a wider X-Y-X angle. The contracting forces, which favor a smaller X-Y-X angle, consist of the orbitals comprising the nonbonding electrons on the central atom (again, both valence and core electrons). The observed geometry is seen as the balance point between these two sets of forces. A simple interaction-distance model of spreading and contracting forces supports this hypothesis. Highly linear trends are obtained for both the nitrogen trihalides (R(2) = 0.981) and phosphorus trihalides (R(2) = 0.992) when the opposing forces are plotted against each other. These results suggest that a revision of the popular conceptual models (hybridization and VSEPR) of molecular geometry might be appropriate.

  6. Interactive session: alpha emitters, fashion or reality? radionuclides and molecules availability

    International Nuclear Information System (INIS)

    Zimmermann, R.

    2015-01-01

    Full text of publication follows. This introduction to the interactive session will simply be based on statements related to the future of therapy in nuclear medicine with some emphasis on the use of alpha-emitters. Some hypotheses will be developed on topics such as 'How will look nuclear medicine in 2025?', 'Do we have enough information to support the use of alpha in therapy?' 'Does it make sense to develop alpha-labelled molecules without long term financial commitment?', 'Will sufficient amounts of radionuclides available when the drugs will be ready for marketing?', 'Do we know enough about alpha emitters toxicity?', 'Is personalized medicine really the solution of the future of health care?', 'How can we convince authorities about the advantages of alpha labelled molecules?', 'Is the development of alpha RIT more expensive or more difficult than beta RIT?', 'Where are all the beta-emitter under development gone?', 'With alpha-emitters, are we speaking about 2025 or 2050?', 'Will Xofigo be a success?', 'What will be the real role of pharmaceutical companies in radiotherapy?', 'Who are the most afraid about radioactivity, the patients or the authorities?'. The speaker will provide his own opinion about each topic. Will you agree or not with him? What is your opinion? (author)

  7. From N-parameter fractional Brownian motions to N-parameter multifractional Brownian motions

    OpenAIRE

    Herbin, E.

    2005-01-01

    International audience; Multifractional Brownian motion is an extension of the well-known fractional Brownian motion where the H¨older regularity is allowed to vary along the paths. In this paper, two kinds of multi-parameter extensions of mBm are studied: one is isotropic while the other is not. For each of these processes, a moving average representation, a harmonizable representation, and the covariance structure are given. The H¨older regularity is then studied. In particular, the case of...

  8. From fractional Brownian motion to multifractional and multistable motion

    Science.gov (United States)

    Falconer, Kenneth

    2015-03-01

    Fractional Brownian motion, introduced by Benoit Mandelbrot and John Van Ness in 1968, has had a major impact on stochastic processes and their applications. We survey a few of the many developments that have stemmed from their ideas. In particular we discuss the local structure of fractional and multifractional Brownian, stable and multistable processes, emphasising the `diagonal' construction of such processes. In all this, the ubiquity and centrality of fractional Brownian motion is striking.

  9. Small molecule inhibitors of PSD95-nNOS protein-protein interactions as novel analgesics

    Science.gov (United States)

    Lee, Wan-Hung; Xu, Zhili; Ashpole, Nicole M.; Hudmon, Andy; Kulkarni, Pushkar M.; Thakur, Ganesh A.; Lai, Yvonne Y.; Hohmann, Andrea G.

    2015-01-01

    Aberrant increases in NMDA receptor (NMDAR) signaling contributes to central nervous system sensitization and chronic pain by activating neuronal nitric oxide synthase (nNOS) and generating nitric oxide (NO). Because the scaffolding protein postsynaptic density 95kDA (PSD95) tethers nNOS to NMDARs, the PSD95-nNOS complex represents a therapeutic target. Small molecule inhibitors IC87201 (EC5O: 23.94 µM) and ZL006 (EC50: 12.88 µM) directly inhibited binding of purified PSD95 and nNOS proteins in AlphaScreen without altering binding of PSD95 to ErbB4. Both PSD95-nNOS inhibitors suppressed glutamate-induced cell death with efficacy comparable to MK-801. IC87201 and ZL006 preferentially suppressed phase 2A pain behavior in the formalin test and suppressed allodynia induced by intraplantar complete Freund’s adjuvant administration. IC87201 and ZL006 suppressed mechanical and cold allodynia induced by the chemotherapeutic agent paclitaxel (ED50s: 2.47 and 0.93 mg/kg i.p. for IC87201 and ZL006, respectively). Efficacy of PSD95-nNOS disruptors was similar to MK-801. Motor ataxic effects were induced by MK-801 but not by ZL006 or IC87201. Finally, MK-801 produced hyperalgesia in the tail-flick test whereas IC87201 and ZL006 did not alter basal nociceptive thresholds. Our studies establish the utility of using AlphaScreen and purified protein pairs to establish and quantify disruption of protein-protein interactions. Our results demonstrate previously unrecognized antinociceptive efficacy of ZL006 and establish, using two small molecules, a broad application for PSD95-nNOS inhibitors in treating neuropathic and inflammatory pain. Collectively, our results demonstrate that disrupting PSD95-nNOS protein-protein interactions is effective in attenuating pathological pain without producing unwanted side effects (i.e. motor ataxia) associated with NMDAR antagonists. PMID:26071110

  10. Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy.

    Science.gov (United States)

    Dias, Raquel; Kolazckowski, Bryan

    2015-11-01

    Interactions between proteins and other molecules play essential roles in all biological processes. Although it is widely held that a protein's ligand specificity is determined primarily by its three-dimensional structure, the general principles by which structure determines ligand binding remain poorly understood. Here we use statistical analyses of a large number of protein-ligand complexes with associated binding-affinity measurements to quantitatively characterize how combinations of atomic interactions contribute to ligand affinity. We find that there are significant differences in how atomic interactions determine ligand affinity for proteins that bind small chemical ligands, those that bind DNA/RNA and those that interact with other proteins. Although protein-small molecule and protein-DNA/RNA binding affinities can be accurately predicted from structural data, models predicting one type of interaction perform poorly on the others. Additionally, the particular combinations of atomic interactions required to predict binding affinity differed between small-molecule and DNA/RNA data sets, consistent with the conclusion that the structural bases determining ligand affinity differ among interaction types. In contrast to what we observed for small-molecule and DNA/RNA interactions, no statistical models were capable of predicting protein-protein affinity with >60% correlation. We demonstrate the potential usefulness of protein-DNA/RNA binding prediction as a possible tool for high-throughput virtual screening to guide laboratory investigations, suggesting that quantitative characterization of diverse molecular interactions may have practical applications as well as fundamentally advancing our understanding of how molecular structure translates into function. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

  11. Interaction of Proliferating Cell Nuclear Antigen With DNA at the Single Molecule Level

    KAUST Repository

    Raducanu, Vlad-Stefan

    2016-05-01

    Proliferating cell nuclear antigen (PCNA) is a key factor involved in Eukaryotic DNA replication and repair, as well as other cellular pathways. Its importance comes mainly from two aspects: the large numbers of interacting partners and the mechanism of facilitated diffusion along the DNA. The large numbers of interacting partners makes PCNA a necessary factor to consider when studying DNA replication, either in vitro or in vivo. The mechanism of facilitated diffusion along the DNA, i.e. sliding along the duplex, reduces the six degrees of freedom of the molecule, three degrees of freedom of translation and three degrees of freedom of rotation, to only two, translation along the duplex and rotational tracking of the helix. Through this mechanism PCNA can recruit its partner proteins and localize them to the right spot on the DNA, maybe in the right spatial orientation, more effectively and in coordination with other proteins. Passive loading of the closed PCNA ring on the DNA without free ends is a topologically forbidden process. Replication factor C (RFC) uses energy of ATP hydrolysis to mechanically open the PCNA ring and load it on the dsDNA. The first half of the introduction gives overview of PCNA and RFC and the loading mechanism of PCNA on dsDNA. The second half is dedicated to a diffusion model and to an algorithm for analyzing PCNA sliding. PCNA and RFC were successfully purified, simulations and a mean squared displacement analysis algorithm were run and showed good stability and experimental PCNA sliding data was analyzed and led to parameters similar to the ones in literature.

  12. Quantum chemical analysis explains hemagglutinin peptide-MHC Class II molecule HLA-DRβ1*0101 interactions

    International Nuclear Information System (INIS)

    Cardenas, Constanza; Villaveces, Jose Luis; Bohorquez, Hugo; Llanos, Eugenio; Suarez, Carlos; Obregon, Mateo; Patarroyo, Manuel Elkin

    2004-01-01

    We present a new method to explore interactions between peptides and major histocompatibility complex (MHC) molecules using the resultant vector of the three principal multipole terms of the electrostatic field expansion. Being that molecular interactions are driven by electrostatic interactions, we applied quantum chemistry methods to better understand variations in the electrostatic field of the MHC Class II HLA-DRβ1*0101-HA complex. Multipole terms were studied, finding strong alterations of the field in Pocket 1 of this MHC molecule, and weak variations in other pockets, with Pocket 1 >> Pocket 4 > Pocket 9 ∼ Pocket 7 > Pocket 6. Variations produced by 'ideal' amino acids and by other occupying amino acids were compared. Two types of interactions were found in all pockets: a strong unspecific one (global interaction) and a weak specific interaction (differential interaction). Interactions in Pocket 1, the dominant pocket for this allele, are driven mainly by the quadrupole term, confirming the idea that aromatic rings are important in these interactions. Multipolar analysis is in agreement with experimental results, suggesting quantum chemistry methods as an adequate methodology to understand these interactions

  13. Suppression of Magnetic Quantum Tunneling in a Chiral Single-Molecule Magnet by Ferromagnetic Interactions.

    Science.gov (United States)

    Lippert, Kai-Alexander; Mukherjee, Chandan; Broschinski, Jan-Philipp; Lippert, Yvonne; Walleck, Stephan; Stammler, Anja; Bögge, Hartmut; Schnack, Jürgen; Glaser, Thorsten

    2017-12-18

    Single-molecule magnets (SMMs) retain a magnetization without applied magnetic field for a decent time due to an energy barrier U for spin-reversal. Despite the success to increase U, the difficult to control magnetic quantum tunneling often leads to a decreased effective barrier U eff and a fast relaxation. Here, we demonstrate the influence of the exchange coupling on the tunneling probability in two heptanuclear SMMs hosting the same spin-system with the same high spin ground state S t = 21/2. A chirality-induced symmetry reduction leads to a switch of the Mn III -Mn III exchange from antiferromagnetic in the achiral SMM [Mn III 6 Cr III ] 3+ to ferromagnetic in the new chiral SMM RR [Mn III 6 Cr III ] 3+ . Multispin Hamiltonian analysis by full-matrix diagonalization demonstrates that the ferromagnetic interactions in RR [Mn III 6 Cr III ] 3+ enforce a well-defined S t = 21/2 ground state with substantially less mixing of M S substates in contrast to [Mn III 6 Cr III ] 3+ and no tunneling pathways below the top of the energy barrier. This is experimentally verified as U eff is smaller than the calculated energy barrier U in [Mn III 6 Cr III ] 3+ due to tunneling pathways, whereas U eff equals U in RR [Mn III 6 Cr III ] 3+ demonstrating the absence of quantum tunneling.

  14. A program for calculating and plotting soft x-ray optical interaction coefficients for molecules

    International Nuclear Information System (INIS)

    Thomas, M.M.; Davis, J.C.; Jacobsen, C.J.; Perera, R.C.C.

    1989-08-01

    Comprehensive tables for atomic scattering factor components, f1 and f2, were compiled by Henke et al. for the extended photon region 50 - 10000 eV. Accurate calculations of optical interaction coefficients for absorption, reflection and scattering by material systems (e.g. filters, multi-layers, etc...), which have widespread application, can be based simply upon the atomic scattering factors for the elements comprising the material, except near the absorption threshold energies. These calculations based upon the weighted sum of f1 and f2 for each atomic species present can be very tedious if done by hand. This led us to develop a user friendly program to perform these calculations on an IBM PC or compatible computer. By entering the chemical formula, density and thickness of up to six molecules, values of the f1, f2, mass absorption transmission efficiencies, attenuation lengths, mirror reflectivities and complex indices of refraction can be calculated and plotted as a function of energy or wavelength. This program will be available distribution. 7 refs., 1 fig

  15. Quantitative affinity electrophoresis of RNA-small molecule interactions by cross-linking the ligand to acrylamide.

    Science.gov (United States)

    Boodram, Sherry N; McCann, Lucas C; Organ, Michael G; Johnson, Philip E

    2013-11-15

    We show that the affinity electrophoresis analysis of RNA-small molecule interactions can be made quantifiable by cross-linking the ligand to the gel matrix. Using an RNA-aminoglycoside model system to verify our method, we attached an acryloyl chloride molecule to the aminoglycosides paromomycin and neomycin B to synthesize an acrylamide-aminoglycoside monomer. This molecule was then used as a component in gel polymerization for affinity electrophoresis, covalently attaching an aminoglycoside molecule to the gel matrix. To test RNA binding to the cross-linked aminoglycosides, we used the aminoglycoside binding RNA molecule derived from thymidylate synthase messenger RNA (mRNA) that contains a C-C mismatch. Binding is indicated by the difference in RNA mobility between gels with cross-linked ligand, with ligand embedded during polymerization, and with no ligand present. Critically, the predicted straight line relationship between the reciprocal of the relative migration of the RNA and the ligand concentration is obtained when using cross-linked aminoglycosides, whereas a straight line is not obtained using embedded aminoglycosides. Average apparent dissociation constants are determined from the slope of the line from these plots. This method allows an easy quantitative comparison between different nucleic acid molecules for a small molecule ligand. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. EVAPORATION: a new vapor pressure estimation method for organic molecules including non-additivity and intramolecular interactions

    Science.gov (United States)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-04-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict vapour pressure p0 of organic molecules needing only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: carbonyls, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  17. The interaction of linear and ring forms of DNA molecules with nanodiamonds synthesized by detonation

    International Nuclear Information System (INIS)

    Purtov, K V; Burakova, L P; Puzyr, A P; Bondar, V S

    2008-01-01

    Nanodiamonds synthesized by detonation have been found not to immobilize the ring form of pUC19 plasmid DNA. Linear pUC19 molecules with blunt ends, prepared by restriction of the initial ring form of pUC19 DNA, and linear 0.25-10 kb DNA fragments are adsorbed on nanodiamonds. The amount of adsorbed linear DNA molecules depends on the size of the molecules and the size of the nanodiamond clusters

  18. Langevin theory of anomalous Brownian motion made simple

    International Nuclear Information System (INIS)

    Tothova, Jana; Vasziova, Gabriela; Lisy, VladimIr; Glod, Lukas

    2011-01-01

    During the century from the publication of the work by Einstein (1905 Ann. Phys. 17 549) Brownian motion has become an important paradigm in many fields of modern science. An essential impulse for the development of Brownian motion theory was given by the work of Langevin (1908 C. R. Acad. Sci., Paris 146 530), in which he proposed an 'infinitely more simple' description of Brownian motion than that by Einstein. The original Langevin approach has however strong limitations, which were rigorously stated after the creation of the hydrodynamic theory of Brownian motion (1945). Hydrodynamic Brownian motion is a special case of 'anomalous Brownian motion', now intensively studied both theoretically and in experiments. We show how some general properties of anomalous Brownian motion can be easily derived using an effective method that allows one to convert the stochastic generalized Langevin equation into a deterministic Volterra-type integro-differential equation for the mean square displacement of the particle. Within the Gibbs statistics, the method is applicable to linear equations of motion with any kind of memory during the evolution of the system. We apply it to memoryless Brownian motion in a harmonic potential well and to Brownian motion in fluids, taking into account the effects of hydrodynamic memory. Exploring the mathematical analogy between Brownian motion and electric circuits, which are at nanoscales also described by the generalized Langevin equation, we calculate the fluctuations of charge and current in RLC circuits that are in contact with the thermal bath. Due to the simplicity of our approach it could be incorporated into graduate courses of statistical physics. Once the method is established, it allows bringing to the attention of students and effectively solving a number of attractive problems related to Brownian motion.

  19. Small molecule inhibition of CBP/catenin interactions eliminates drug resistant clones in acute lymphoblastic leukemia

    Science.gov (United States)

    Gang, Eun Ji; Hsieh, Yao-Te; Pham, Jennifer; Zhao, Yi; Nguyen, Cu; Huantes, Sandra; Park, Eugene; Naing, Khatija; Klemm, Lars; Swaminathan, Srividya; Conway, Edward M.; Pelus, Louis M.; Crispino, John; Mullighan, Charles; McMillan, Michael; Müschen, Markus; Kahn, Michael; Kim, Yong-Mi

    2014-01-01

    Drug resistance in acute lymphoblastic leukemia (ALL) remains a major problem warranting new treatment strategies. Wnt/catenin signaling is critical for the self-renewal of normal hematopoietic progenitor cells. Deregulated Wnt signaling is evident in chronic and acute myeloid leukemia, however little is known about ALL. Differential interaction of catenin with either the Kat3 coactivator CREBBP (CBP) or the highly homologous EP300 (p300) is critical to determine divergent cellular responses and provides a rationale for the regulation of both proliferation and differentiation by the Wnt signaling pathway. Usage of the coactivator CBP by catenin leads to transcriptional activation of cassettes of genes that are involved in maintenance of progenitor cell self-renewal. However, the use of the coactivator p300, leads to activation of genes involved in the initiation of differentiation. ICG-001 is a novel small molecule modulator of Wnt/catenin signaling, which specifically binds to the N-terminus of CBP and not p300, within amino acids 1–110, thereby disrupting the interaction between CBP and catenin. Here, we report that selective disruption of the CBP/β- and γ-catenin interactions using ICG-001 leads to differentiation of pre-B ALL cells and loss of self-renewal capacity. Survivin, an inhibitor-of-apoptosis protein, was also downregulated in primary ALL after treatment with ICG-001. Using ChIP assay, we demonstrate occupancy by CBP of the survivin promoter, which is decreased by ICG-001 in primary ALL. CBP-mutations have been recently identified in a significant percentage of ALL patients, however, almost all of the identified mutations reported occur C-terminal to the binding site for ICG-001. Importantly, ICG-001, regardless of CBP mutational status and chromosomal aberration, leads to eradication of drug-resistant primary leukemia in combination with conventional therapy in vitro and significantly prolongs the survival of NOD/SCID mice engrafted with primary

  20. The relativistic Brownian motion: Interdisciplinary applications

    International Nuclear Information System (INIS)

    Aragones-Munoz, A; Sandoval-Villalbazo, A

    2010-01-01

    Relativistic Brownian motion theory will be applied to the study of analogies between physical and economic systems, emphasizing limiting cases in which Gaussian distributions are no longer valid. The characteristic temperatures of the particles will be associated with the concept of variance, and this will allow us to choose whether the pertinent distribution is classical or relativistic, while working specific situations. The properties of particles can be interpreted as economic variables, in order to study the behavior of markets in terms of Levy financial processes, since markets behave as stochastic systems. As far as we know, the application of the Juettner distribution to the study of economic systems is a new idea.

  1. Multifragmentation with Brownian one-body dynamics

    International Nuclear Information System (INIS)

    Guarnera, A.; Chomaz, PH.; Colonna, M.; Chomaz, PH.; Guarnera, A.

    1996-01-01

    A first application is made of Brownian one-body dynamics to nuclear multifragmentation. A gold nucleus is compressed to double density and then let free to evolve under the combined influence of the effective one-body field and the residual two-body collision processes, with the effects of the fluctuations included whenever local spinodal instability occurs. The system quickly expands into a hollow and unstable configuration which transforms into several intermediate-mass fragments. The analysis of the resulting fragment pattern suggests that the model provides a physically reasonable description of nuclear multifragmentation processes. (authors)

  2. Time-averaged MSD of Brownian motion

    Science.gov (United States)

    Andreanov, Alexei; Grebenkov, Denis S.

    2012-07-01

    We study the statistical properties of the time-averaged mean-square displacements (TAMSD). This is a standard non-local quadratic functional for inferring the diffusion coefficient from an individual random trajectory of a diffusing tracer in single-particle tracking experiments. For Brownian motion, we derive an exact formula for the Laplace transform of the probability density of the TAMSD by mapping the original problem onto chains of coupled harmonic oscillators. From this formula, we deduce the first four cumulant moments of the TAMSD, the asymptotic behavior of the probability density and its accurate approximation by a generalized Gamma distribution.

  3. Elementary electron-molecule interactions and negative ion resonances at subexcitation energies and their significance in gaseous dielectrics

    International Nuclear Information System (INIS)

    Christophorou, L.G.

    1977-01-01

    Recent knowledge on low-energy (mostly approximately less than 10 eV) electron-molecule interaction processes in dilute and in dense gases is synthesized, discussed, and related to the breakdown strength of gaseous dielectrics. Optimal design of multicomponent gaseous insulators can be made on the basis of such knowledge

  4. A quantitative assay to measure the interaction between immunogenic peptides and purified class I major histocompatibility complex molecules

    DEFF Research Database (Denmark)

    Olsen, A C; Pedersen, L O; Hansen, A S

    1994-01-01

    A direct and sensitive biochemical assay to measure the interaction in solution between peptides and affinity-purified major histocompatibility complex (MHC) class I molecules has been generated. Specific binding reflecting the known class I restriction of cytotoxic T cell responses was obtained...

  5. Interaction of slow electrons with high-pressure gases ('Quasi-liquids'): synthesis of our knowledge on slow electron-molecule interactions. Progress report

    International Nuclear Information System (INIS)

    McCorkle, D.L.; Christophorou, L.G.

    1985-01-01

    A crucial step in our efforts to develop not only a coherent picture of radiation interaction with matter, but also to understand radiation effects and mechanisms, as well as the effects of chemical pollutants and toxic compounds, is to relate the often abundant knowledge on isolated molecules (low pressure gases) to that on liquids or solids. To understand the roles of the physical and chemical properties of molecules in biological reactions, we must know how these isolated-molecule properties change as molecules are embedded in gradually thicker and thicker (denser and denser) gaseous and, finally, liquid environments. The work initiated by us both at the Physics Department of The University of Tennessee and at the Oak Ridge National Laboratory addresses itself to this question. At both places, high pressure (40 to approx.8000 kPa) electron swarm experiments are currently in operation yielding information as to the effects of the density and nature of the environment on fundamental electron-molecule interaction processes at densities intermediate to those corresponding to low pressure gases and liquids, and the gradual transition from isolated molecule to condensed phase behavior

  6. Interactions of DNA binding proteins with G-Quadruplex structures at the single molecule level

    Science.gov (United States)

    Ray, Sujay

    Guanine-rich nucleic acid (DNA/RNA) sequences can form non-canonical secondary structures, known as G-quadruplex (GQ). Numerous in vivo and in vitro studies have demonstrated formation of these structures in telomeric and non-telomeric regions of the genome. Telomeric GQs protect the chromosome ends whereas non-telomeric GQs either act as road blocks or recognition sites for DNA metabolic machinery. These observations suggest the significance of these structures in regulation of different metabolic processes, such as replication and repair. GQs are typically thermodynamically more stable than the corresponding Watson-Crick base pairing formed by G-rich and C-rich strands, making protein activity a crucial factor for their destabilization. Inside the cell, GQs interact with different proteins and their enzymatic activity is the determining factor for their stability. We studied interactions of several proteins with GQs to understand the underlying principles of protein-GQ interactions using single-molecule FRET and other biophysical techniques. Replication Protein-A (RPA), a single stranded DNA (ssDNA) binding protein, is known to posses GQ unfolding activity. First, we compared the thermal stability of three potentially GQ-forming DNA sequences (PQS) to their stability against RPA-mediated unfolding. One of these sequences is the human telomeric repeat and the other two, located in the promoter region of tyrosine hydroxylase gene, are highly heterogeneous sequences that better represent PQS in the genome. The thermal stability of these structures do not necessarily correlate with their stability against protein-mediated unfolding. We conclude that thermal stability is not necessarily an adequate criterion for predicting the physiological viability of GQ structures. To determine the critical structural factors that influence protein-GQ interactions we studied two groups of GQ structures that have systematically varying loop lengths and number of G-tetrad layers. We

  7. Atom-molecule equilibration in a degenerate Fermi gas with resonant interactions

    DEFF Research Database (Denmark)

    Williams, J. E.; Nikuni, T.; Nygaard, Nicolai

    2004-01-01

    We present a nonequilibrium kinetic theory describing atom-molecule population dynamics in a two-component Fermi gas with a Feshbach resonance. Key collision integrals emerge that govern the relaxation of the atom-molecule mixture to chemical and thermal equilibrium. Our focus is on the pseudogap...

  8. Diffusion in one dimensional random medium and hyperbolic Brownian motion

    International Nuclear Information System (INIS)

    Comtet, A.; Monthus, C.; Paris-6 Univ., 75

    1995-03-01

    Classical diffusion in a random medium involves an exponential functional of Brownian motion. This functional also appears in the study of Brownian diffusion on a Riemann surface of constant negative curvature. This relationship is analyzed in detail and various distributions are studied using stochastic calculus and functional integration. (author) 17 refs

  9. Fractional Brownian motion of director fluctuations in nematic ordering

    DEFF Research Database (Denmark)

    Zhang, Z.; Mouritsen, Ole G.; Otnes, K.

    1993-01-01

    to determine the Hurst exponent H. Theory and experiment are in good agreement. A value of H congruent-to 1 was found for the nematic phase, characterizing fractional Brownian motion, whereas H congruent-to 0.5, reflecting ordinary Brownian motion, applies in the isotropic phase. Field-induced crossover from...

  10. Brownian motion of a particle with arbitrary shape.

    Science.gov (United States)

    Cichocki, Bogdan; Ekiel-Jeżewska, Maria L; Wajnryb, Eligiusz

    2015-06-07

    Brownian motion of a particle with an arbitrary shape is investigated theoretically. Analytical expressions for the time-dependent cross-correlations of the Brownian translational and rotational displacements are derived from the Smoluchowski equation. The role of the particle mobility center is determined and discussed.

  11. CNT based thermal Brownian motor to pump water in nanodevices

    DEFF Research Database (Denmark)

    Oyarzua, Elton; Zambrano, Harvey; Walther, Jens Honore

    2016-01-01

    Brownian molecular motors are nanoscale machines that exploit thermal fluctuations for directional motion by employing mechanisms such as the Feynman-Smoluchowski ratchet. In this study, using Non Equilibrium Molecular Dynamics, we propose a novel thermal Brownian motor for pumping water through ...

  12. Magnetic nanoparticle thermometry independent of Brownian relaxation

    Science.gov (United States)

    Zhong, Jing; Schilling, Meinhard; Ludwig, Frank

    2018-01-01

    An improved method of magnetic nanoparticle (MNP) thermometry is proposed. The phase lag ϕ of the fundamental f 0 harmonic is measured to eliminate the influence of Brownian relaxation on the ratio of 3f 0 to f 0 harmonic amplitudes applying a phenomenological model, thus allowing measurements in high-frequency ac magnetic fields. The model is verified by simulations of the Fokker–Planck equation. An MNP spectrometer is calibrated for the measurements of the phase lag ϕ and the amplitudes of 3f 0 and f 0 harmonics. Calibration curves of the harmonic ratio and tanϕ are measured by varying the frequency (from 10 Hz to 1840 Hz) of ac magnetic fields with different amplitudes (from 3.60 mT to 4.00 mT) at a known temperature. A phenomenological model is employed to fit the calibration curves. Afterwards, the improved method is proposed to iteratively compensate the measured harmonic ratio with tanϕ, and consequently calculate temperature applying the static Langevin function. Experimental results on SHP-25 MNPs show that the proposed method significantly improves the systematic error to 2 K at maximum with a relative accuracy of about 0.63%. This demonstrates the feasibility of the proposed method for MNP thermometry with SHP-25 MNPs even if the MNP signal is affected by Brownian relaxation.

  13. Nonequilibrium Brownian Motion beyond the Effective Temperature

    Science.gov (United States)

    Gnoli, Andrea; Puglisi, Andrea; Sarracino, Alessandro; Vulpiani, Angelo

    2014-01-01

    The condition of thermal equilibrium simplifies the theoretical treatment of fluctuations as found in the celebrated Einstein’s relation between mobility and diffusivity for Brownian motion. Several recent theories relax the hypothesis of thermal equilibrium resulting in at least two main scenarios. With well separated timescales, as in aging glassy systems, equilibrium Fluctuation-Dissipation Theorem applies at each scale with its own “effective” temperature. With mixed timescales, as for example in active or granular fluids or in turbulence, temperature is no more well-defined, the dynamical nature of fluctuations fully emerges and a Generalized Fluctuation-Dissipation Theorem (GFDT) applies. Here, we study experimentally the mixed timescale regime by studying fluctuations and linear response in the Brownian motion of a rotating intruder immersed in a vibro-fluidized granular medium. Increasing the packing fraction, the system is moved from a dilute single-timescale regime toward a denser multiple-timescale stage. Einstein’s relation holds in the former and is violated in the latter. The violation cannot be explained in terms of effective temperatures, while the GFDT is able to impute it to the emergence of a strong coupling between the intruder and the surrounding fluid. Direct experimental measurements confirm the development of spatial correlations in the system when the density is increased. PMID:24714671

  14. Nonequilibrium Brownian motion beyond the effective temperature.

    Directory of Open Access Journals (Sweden)

    Andrea Gnoli

    Full Text Available The condition of thermal equilibrium simplifies the theoretical treatment of fluctuations as found in the celebrated Einstein's relation between mobility and diffusivity for Brownian motion. Several recent theories relax the hypothesis of thermal equilibrium resulting in at least two main scenarios. With well separated timescales, as in aging glassy systems, equilibrium Fluctuation-Dissipation Theorem applies at each scale with its own "effective" temperature. With mixed timescales, as for example in active or granular fluids or in turbulence, temperature is no more well-defined, the dynamical nature of fluctuations fully emerges and a Generalized Fluctuation-Dissipation Theorem (GFDT applies. Here, we study experimentally the mixed timescale regime by studying fluctuations and linear response in the Brownian motion of a rotating intruder immersed in a vibro-fluidized granular medium. Increasing the packing fraction, the system is moved from a dilute single-timescale regime toward a denser multiple-timescale stage. Einstein's relation holds in the former and is violated in the latter. The violation cannot be explained in terms of effective temperatures, while the GFDT is able to impute it to the emergence of a strong coupling between the intruder and the surrounding fluid. Direct experimental measurements confirm the development of spatial correlations in the system when the density is increased.

  15. The lines-of-force landscape of interactions between molecules in crystals; cohesive versus tolerant and 'collateral damage' contact.

    Science.gov (United States)

    Gavezzotti, Angelo

    2010-06-01

    A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule-molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in approximately 9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO(2), SO(2)). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom-atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care.

  16. Alteration of RNA splicing by small molecule inhibitors of the interaction between NHP2L1 and U4

    Science.gov (United States)

    Diouf, Barthelemy; Lin, Wenwei; Goktug, Asli; Grace, Christy R. R.; Waddell, Michael Brett; Bao, Ju; Shao, Youming; Heath, Richard J.; Zheng, Jie J.; Shelat, Anang A.; Relling, Mary V.; Chen, Taosheng; Evans, William E.

    2018-01-01

    Splicing is an important eukaryotic mechanism for expanding the transcriptome and proteome, influencing a number of biological processes. Understanding its regulation and identifying small molecules that modulate this process remains a challenge. We developed an assay based on time-resolved FRET (TR-FRET) to detect the interaction between the protein NHP2L1 and U4 RNA, which are two key components of the spliceosome. We used this assay to identify small molecules that interfere with this interaction in a high-throughput screening (HTS) campaign. Topotecan and other camptothecin derivatives were among the top hits. We confirmed that topotecan disrupts the interaction between NHP2L1 and U4 by binding to U4 and inhibits RNA splicing. Our data reveal new functions of known drugs which could facilitate the development of therapeutic strategies to modify splicing and alter gene function. PMID:28985478

  17. Self-induced temperature gradients in Brownian dynamics

    Science.gov (United States)

    Devine, Jack; Jack, M. W.

    2017-12-01

    Brownian systems often surmount energy barriers by absorbing and emitting heat to and from their local environment. Usually, the temperature gradients created by this heat exchange are assumed to dissipate instantaneously. Here we relax this assumption to consider the case where Brownian dynamics on a time-independent potential can lead to self-induced temperature gradients. In the same way that externally imposed temperature gradients can cause directed motion, these self-induced gradients affect the dynamics of the Brownian system. The result is a coupling between the local environment and the Brownian subsystem. We explore the resulting dynamics and thermodynamics of these coupled systems and develop a robust method for numerical simulation. In particular, by focusing on one-dimensional situations, we show that self-induced temperature gradients reduce barrier-crossing rates. We also consider a heat engine and a heat pump based on temperature gradients induced by a Brownian system in a nonequilibrium potential.

  18. Level-statistics in Disordered Systems: A single parametric scaling and Connection to Brownian Ensembles

    OpenAIRE

    Shukla, Pragya

    2004-01-01

    We find that the statistics of levels undergoing metal-insulator transition in systems with multi-parametric Gaussian disorders and non-interacting electrons behaves in a way similar to that of the single parametric Brownian ensembles \\cite{dy}. The latter appear during a Poisson $\\to$ Wigner-Dyson transition, driven by a random perturbation. The analogy provides the analytical evidence for the single parameter scaling of the level-correlations in disordered systems as well as a tool to obtai...

  19. Intense Interactions of Molecules with a Short-Wavelength Electromagnetic Radiation Field: II. Resonance Scattering of Radiation and Fluorescence

    Science.gov (United States)

    Pegarkov, A. I.

    2001-07-01

    Within the framework of the nonadiabatic approach developed in the preceding paper, the resonance scattering, resonance Raman scattering, and resonance fluorescence are studied in detail for diatomic and triatomic molecules, and polyatomic symmetric and antisymmetric top molecules, which interact with the field of short-wavelength radiation with a wavelength λ ≥ Å and an intensity up to 1014 W/cm2. The coherent excitations of high-lying Rydberg and autoionizing states are taken into account. Analytical expressions for calculating the tensors and cross sections of the above processes are derived.

  20. Resonance reactions and enhancement of weak interactions in collisions of cold molecules

    International Nuclear Information System (INIS)

    Flambaum, V. V.; Ginges, J. S. M.

    2006-01-01

    With the creation of ultracold atoms and molecules, a new type of chemistry - 'resonance' chemistry - emerges: chemical reactions can occur when the energy of colliding atoms and molecules matches a bound state of the combined molecule (Feshbach resonance). This chemistry is rather similar to reactions that take place in nuclei at low energies. In this paper we suggest some problems for future experimental and theoretical work related to the resonance chemistry of ultracold molecules. Molecular Bose-Einstein condensates are particularly interesting because in this system collisions and chemical reactions are extremely sensitive to weak fields; also, a preferred reaction channel may be enhanced due to a finite number of final states. The sensitivity to weak fields arises due to the high density of narrow compound resonances and the macroscopic number of molecules with kinetic energy E=0 (in the ground state of a mean-field potential). The high sensitivity to the magnetic field may be used to measure the distribution of energy intervals, widths, and magnetic moments of compound resonances and study the onset of quantum chaos. A difference in the production rate of right-handed and left-handed chiral molecules may be produced by external electric E and magnetic B fields and the finite width Γ of the resonance (correlation ΓE·B). The same effect may be produced by the parity-violating energy difference in chiral molecules

  1. (CryoTransmission Electron Microscopy of Phospholipid Model Membranes Interacting with Amphiphilic and Polyphilic Molecules

    Directory of Open Access Journals (Sweden)

    Annette Meister

    2017-10-01

    Full Text Available Lipid membranes can incorporate amphiphilic or polyphilic molecules leading to specific functionalities and to adaptable properties of the lipid bilayer host. The insertion of guest molecules into membranes frequently induces changes in the shape of the lipid matrix that can be visualized by transmission electron microscopy (TEM techniques. Here, we review the use of stained and vitrified specimens in (cryoTEM to characterize the morphology of amphiphilic and polyphilic molecules upon insertion into phospholipid model membranes. Special emphasis is placed on the impact of novel synthetic amphiphilic and polyphilic bolalipids and polymers on membrane integrity and shape stability.

  2. High-Affinity Small-Molecule Inhibitors of the Menin-Mixed Lineage Leukemia (MLL) Interaction Closely Mimic a Natural Protein-Protein Interaction

    Energy Technology Data Exchange (ETDEWEB)

    He, Shihan; Senter, Timothy J.; Pollock, Jonathan; Han, Changho; Upadhyay, Sunil Kumar; Purohit, Trupta; Gogliotti, Rocco D.; Lindsley, Craig W.; Cierpicki, Tomasz; Stauffer, Shaun R.; Grembecka, Jolanta [Michigan; (Vanderbilt); (Vanderbilt-MED)

    2014-10-02

    The protein–protein interaction (PPI) between menin and mixed lineage leukemia (MLL) plays a critical role in acute leukemias, and inhibition of this interaction represents a new potential therapeutic strategy for MLL leukemias. We report development of a novel class of small-molecule inhibitors of the menin–MLL interaction, the hydroxy- and aminomethylpiperidine compounds, which originated from HTS of ~288000 small molecules. We determined menin–inhibitor co-crystal structures and found that these compounds closely mimic all key interactions of MLL with menin. Extensive crystallography studies combined with structure-based design were applied for optimization of these compounds, resulting in MIV-6R, which inhibits the menin–MLL interaction with IC50 = 56 nM. Treatment with MIV-6 demonstrated strong and selective effects in MLL leukemia cells, validating specific mechanism of action. Our studies provide novel and attractive scaffold as a new potential therapeutic approach for MLL leukemias and demonstrate an example of PPI amenable to inhibition by small molecules.

  3. Separation and Characterization of DNA Molecules and Intermolecular Interactions in Pressure-Driven Micro Flow

    Science.gov (United States)

    Friedrich, Sarah; Wang, Tza-Huei

    Pressure-driven flow in micron-sized diameter capillaries can be used to separate DNA molecules by size in a technique called Free Solution Hydrodynamic Separation. By coupling this technique with Cylindrical Illumination Confocal Spectroscopy, we have developed a highly sensitive and quantitative platform capable of separating DNA molecules by length over a large dynamic range (25 bp to 48 kbp) in a single run using only picoliters or femtograms of a DNA sample. The optical detection volume completely spans the capillary cross section, enabling highly efficient single molecule detection for enhanced sensitivity and quantification accuracy via single molecule counting. Because each DNA molecule generates its own fluorescent burst, these burst profiles can be further analyzed to individually characterize each DNA molecule's shape as it passes through the detection region. We exploit these burst profiles to visualize fluctuations in conformation under shear flow in microcapillaries, and utilizing combined mobility shift analysis, explore the complex relationship between molecular properties including length and conformation, hydrodynamic mobility, solution conditions including ion species and concentrations, and separation conditions including flow rate and capillary diameter.

  4. Electrostatic similarities between protein and small molecule ligands facilitate the design of protein-protein interaction inhibitors.

    Directory of Open Access Journals (Sweden)

    Arnout Voet

    Full Text Available One of the underlying principles in drug discovery is that a biologically active compound is complimentary in shape and molecular recognition features to its receptor. This principle infers that molecules binding to the same receptor may share some common features. Here, we have investigated whether the electrostatic similarity can be used for the discovery of small molecule protein-protein interaction inhibitors (SMPPIIs. We have developed a method that can be used to evaluate the similarity of electrostatic potentials between small molecules and known protein ligands. This method was implemented in a software called EleKit. Analyses of all available (at the time of research SMPPII structures indicate that SMPPIIs bear some similarities of electrostatic potential with the ligand proteins of the same receptor. This is especially true for the more polar SMPPIIs. Retrospective analysis of several successful SMPPIIs has shown the applicability of EleKit in the design of new SMPPIIs.

  5. Modification in structure, phase transition, and magnetic property of metallic gallium driven by atom-molecule interactions.

    Science.gov (United States)

    Song, Le Xin; Chen, Jie; Zhu, Lin Hong; Xia, Juan; Yang, Jun

    2011-09-05

    The present work supports a novel paradigm in which the surface structure and stacking behavior of metallic gallium (Ga) were significantly influenced by the preparation process in the presence of organic small molecules (ethanol, acetone, dichloromethane, and diethyl ether). The extent of the effect strongly depends on the polarity of the molecules. Especially, a series of new atom-molecule aggregates consisting of metallic Ga and macrocyclic hosts (cyclodextrins, CDs) were prepared and characterized by various techniques. A comprehensive comparative analysis between free metallic Ga and the Ga samples obtained provides important and at present rare information on the modification in structure, phase transition, and magnetic property of Ga driven by atom-molecule interactions. First, there is a notable difference in microstructure and electronic structure between the different types of Ga samples. Second, differential scanning calorimetry analysis gives us a complete picture (such as the occurrence of a series of metastable phases of Ga in the presence of CDs) that has allowed us to consider that Ga atoms were protected by the shielding effect provided by the cavities of CDs. Third, the metallic Ga distributed in the aggregates exhibits very interesting magnetic property compared to free metallic Ga, such as the uniform zero-field-cooled and field-cooled magnetization processes, the enhanced responses in magnetization to temperature and applied field, and the fundamental change in shape of magnetic hysteresis loops. These significant changes in structural transformation and physical property of Ga provide a novel insight into the understanding of atom-molecule interactions between metallic atoms and organic molecules.

  6. Fractional Brownian motion and multifractional Brownian motion of Riemann-Liouville type

    Science.gov (United States)

    Lim, S. C.

    2001-02-01

    The relationship between standard fractional Brownian motion (FBM) and FBM based on the Riemann-Liouville fractional integral (or RL-FBM) is clarified. The absence of stationary property in the increment process of RL-FBM is compensated by a weaker property of local stationarity, and the stationary property for the increments of the large-time asymptotic RL-FBM. Generalization of RL-FBM to the RL-multifractional Brownian motion (RL-MBM) can be carried out by replacing the constant Hölder exponent by a time-dependent function. RL-MBM is shown to satisfy a weaker scaling property known as the local asymptotic self-similarity. This local scaling property can be translated into the small-scale behaviour of the associated scalogram by using the wavelet transform.

  7. Photo-cross-linked small-molecule microarrays as chemical genomic tools for dissecting protein-ligand interactions.

    Science.gov (United States)

    Kanoh, Naoki; Asami, Aya; Kawatani, Makoto; Honda, Kaori; Kumashiro, Saori; Takayama, Hiroshi; Simizu, Siro; Amemiya, Tomoyuki; Kondoh, Yasumitsu; Hatakeyama, Satoru; Tsuganezawa, Keiko; Utata, Rei; Tanaka, Akiko; Yokoyama, Shigeyuki; Tashiro, Hideo; Osada, Hiroyuki

    2006-12-18

    We have developed a unique photo-cross-linking approach for immobilizing a variety of small molecules in a functional-group-independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on-array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo-cross-linked microarrays of about 2000 natural products and drugs were constructed. This photo-cross-linked microarray format was found to be useful not merely for ligand screening but also to study the structure-activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo-cross-linking process.

  8. 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.

  9. Brownian motion with multiplicative noises revisited

    International Nuclear Information System (INIS)

    Kuroiwa, T; Miyazaki, K

    2014-01-01

    The Langevin equation with multiplicative noise and a state-dependent transport coefficient should always complemented with the proper interpretation rule of the noise, such as the Itô and Stratonovich conventions. Although the mathematical relationship between the different rules and how to translate from one rule to another are well established, the subject of which is a more physically natural rule still remains controversial. In this communication, we derive the overdamped Langevin equation with multiplicative noise for Brownian particles, by systematically eliminating the fast degrees of freedom of the underdamped Langevin equation. The Langevin equations obtained here vary depending on the choice of the noise conventions but they are different representations for an identical phenomenon. The results apply to multi-variable, nonequilibrium, non-stationary systems, and other general settings. (fast track communication)

  10. Direct Determination of Chitosan–Mucin Interactions Using a Single-Molecule Strategy: Comparison to Alginate–Mucin Interactions

    Directory of Open Access Journals (Sweden)

    Kristin E. Haugstad

    2015-01-01

    Full Text Available Aqueous chitosan possesses attractive interaction capacities with various molecular groups that can be involved in hydrogen bonds and electrostatic and hydrophobic interactions. In the present paper, we report on the direct determination of chitosan–mucin molecular pair interactions at various solvent conditions as compared to alginate–mucin interactions. Two chitosans of high molecular weight with different degrees of acetylation—thus possessing different solubility profiles in aqueous solution as a function of pH and two alginates with different fractions of α-guluronic acid were employed. The interaction properties were determined through a direct unbinding assay at the single-molecular pair level using an atomic force microscope. When probed against immobilized mucin, both chitosans and alginates revealed unbinding profiles characteristic of localized interactions along the polymers. The interaction capacities and estimated parameters of the energy landscapes of the pairwise chitosan–mucin and alginate–mucin interactions are discussed in view of possible contributions from various fundamental forces. Signatures arising both from an electrostatic mechanism and hydrophobic interaction are identified in the chitosan–mucin interaction properties. The molecular nature of the observed chitosan–mucin and alginate–mucin interactions indicates that force spectroscopy provides fundamental insights that can be useful in understanding the surface binding properties of other potentially mucoadhesive polymers.

  11. Relativistic Brownian motion: from a microscopic binary collision model to the Langevin equation.

    Science.gov (United States)

    Dunkel, Jörn; Hänggi, Peter

    2006-11-01

    The Langevin equation (LE) for the one-dimensional relativistic Brownian motion is derived from a microscopic collision model. The model assumes that a heavy pointlike Brownian particle interacts with the lighter heat bath particles via elastic hard-core collisions. First, the commonly known, nonrelativistic LE is deduced from this model, by taking into account the nonrelativistic conservation laws for momentum and kinetic energy. Subsequently, this procedure is generalized to the relativistic case. There, it is found that the relativistic stochastic force is still delta correlated (white noise) but no longer corresponds to a Gaussian white noise process. Explicit results for the friction and momentum-space diffusion coefficients are presented and discussed.

  12. Self-assembly of actin monomers into long filaments: Brownian dynamics simulations

    Science.gov (United States)

    Guo, Kunkun; Shillcock, Julian; Lipowsky, Reinhard

    2009-07-01

    Brownian dynamics simulations are used to study the dynamical process of self-assembly of actin monomers into long filaments containing up to 1000 actin protomers. In order to overcome the large separation of time scales between the diffusive motion of the free monomers and the relatively slow attachment and detachment processes at the two ends of the filaments, we introduce a novel rescaling procedure by which we speed all dynamical processes related to actin polymerization and depolymerization up by the same factor. In general, the actin protomers within a filament can attain three different states corresponding to a bound adenosine triphosphate (ATP), adenosine diphosphate with inorganic phosphate (ADP/P), and ADP molecule. The simplest situation that has been studied experimentally is provided by the polymerization of ADP-actin, for which all protomers are identical. This case is used to unravel certain relations between the filament's physical properties and the model parameters such as the attachment rate constant and the size of the capture zone, the detachment rate and the probability of the detached event, as well as the growth rate and waiting times between two successive attachment/detachment events. When a single filament is allowed to grow in a bath of constant concentration of free ADP-actin monomers, its growth rate increases linearly with the free monomer concentration in quantitative agreement with in vitro experiments. The results also show that the waiting time is governed by exponential distributions and that the two ends of a filament undergo biased random walks. The filament length fluctuations are described by a length diffusion constant that is found to attain a constant value at low ADP-actin concentration and to increase linearly with this concentration. It is straightforward to apply our simulation code to more complex processes such as polymerization of ATP-actin coupled to ATP hydrolysis, force generation by filaments, formation of

  13. Interaction of spin and vibrations in transport through single-molecule magnets.

    Science.gov (United States)

    May, Falk; Wegewijs, Maarten R; Hofstetter, Walter

    2011-01-01

    We study electron transport through a single-molecule magnet (SMM) and the interplay of its anisotropic spin with quantized vibrational distortions of the molecule. Based on numerical renormalization group calculations we show that, despite the longitudinal anisotropy barrier and small transverse anisotropy, vibrational fluctuations can induce quantum spin-tunneling (QST) and a QST-Kondo effect. The interplay of spin scattering, QST and molecular vibrations can strongly enhance the Kondo effect and induce an anomalous magnetic field dependence of vibrational Kondo side-bands.

  14. Interaction of spin and vibrations in transport through single-molecule magnets

    Directory of Open Access Journals (Sweden)

    Falk May

    2011-10-01

    Full Text Available We study electron transport through a single-molecule magnet (SMM and the interplay of its anisotropic spin with quantized vibrational distortions of the molecule. Based on numerical renormalization group calculations we show that, despite the longitudinal anisotropy barrier and small transverse anisotropy, vibrational fluctuations can induce quantum spin-tunneling (QST and a QST-Kondo effect. The interplay of spin scattering, QST and molecular vibrations can strongly enhance the Kondo effect and induce an anomalous magnetic field dependence of vibrational Kondo side-bands.

  15. Light-Matter Interaction Atoms and Molecules in External Fields and Nonlinear Optics

    CERN Document Server

    Hill, Wendell T

    2006-01-01

    This book draws together the principal ideas that form the basis of atomic, molecular, and optical science and engineering. It covers the basics of atoms, diatomic molecules, atoms and molecules in static and electromagnetic fields and nonlinear optics. Exercises and bibliographies supplement each chapter, while several appendices present such important background information as physics and math definitions, atomic and molecular data, and tensor algebra. Accessible to advanced undergraduates, graduate students, or researchers who have been trained in one of the conventional curricula of physic

  16. Surface-supported Ag islands stabilized by a quantum size effect: Their interaction with small molecules relevant to ethylene epoxidation

    Energy Technology Data Exchange (ETDEWEB)

    Shao, Dahai [Iowa State Univ., Ames, IA (United States)

    2013-05-15

    This dissertation focuses on how QSE-stabilized, surface-supported Ag nanoclusters will interact with ethylene or oxygen. Experiments are performed to determine whether the QSE-mediated Ag islands react differently toward adsorption of ethylene or oxygen, or whether the adsorption of these small molecules will affect the QSE-mediated stability of Ag islands. Studies of the interaction of oxygen with Ag/Si(111)-7×7 were previously reported, but these studies were performed at a low Ag coverage where 3D Ag islands were not formed. So the study of such a system at a higher Ag coverage will be a subject of this work. The interaction of ethylene with Ag/Si(111)-7×7, as well as the interaction of oxygen with Ag/NiAl(110) are also important parts of this study.

  17. Interaction of intense electromagnetic fields with SF6 molecules and clusters in supersonic expansion

    International Nuclear Information System (INIS)

    Airoldi, V.J.T.

    1987-01-01

    A method of measuring SF 6 cluster formation and inhibition in pulsed supersonic expansion in the presence of intense electromagnetic radiation is presented. The characterization of the expansion of SF 6 molecules was done and, the extension of the collision region was determined. An improved unidimensional theory of supersonic expansion showed good agreement with the experimental results. The spectra of multiphoton absorption of SF 6 molecules in supersonic jet and the average energy absorved by each molecule were determined. The absorption spectra of molecule in the collision region present absorption maxima different from those obtained in the collisionless region. The results, if compared with the literature data, show good agreement, with a small difference in the spetra corresponding to the collisionless region. This difference was observed, for the first time in the multiphoton absorption and is attribuited to cluster formation in the jet. A new technique for measuring cluster formation in the supersonic jet, based on determination of the spatial distribution of the energy of molecules in the jet after passing through a skimmer located in the collision region is shown. The inhibition of cluster formation, due to the incidence of intense electromagnetic radiation from a CO 2 -TEA pulsed laser in the initial collision region of the jet, causes a second expansion in the skimmer. The results obtained show that this method can lead to a new isotope separation process. All the parts of the experimental set up, for example, high vacuum system, pulsed valve and pyroelectric detector, were developed and constructed specially for the experiment. (Author) [pt

  18. Rab Interacting Molecules 2 and 3 Directly Interact with the Pore-Forming CaV1.3 Ca2+ Channel Subunit and Promote Its Membrane Expression

    OpenAIRE

    Maria M. Picher; Maria M. Picher; Maria M. Picher; Ana-Maria Oprişoreanu; SangYong Jung; SangYong Jung; SangYong Jung; Katrin Michel; Susanne Schoch; Tobias Moser; Tobias Moser; Tobias Moser; Tobias Moser

    2017-01-01

    Rab interacting molecules (RIMs) are multi-domain proteins that positively regulate the number of Ca2+ channels at the presynaptic active zone (AZ). Several molecular mechanisms have been demonstrated for RIM-binding to components of the presynaptic Ca2+ channel complex, the key signaling element at the AZ. Here, we report an interaction of the C2B domain of RIM2α and RIM3γ with the C-terminus of the pore-forming α–subunit of CaV1.3 channels (CaV1.3α1), which mediate stimulus-secretion coupli...

  19. Retention models and interaction mechanisms of benzene and other aromatic molecules with an amylose-based sorbent.

    Science.gov (United States)

    Hsieh, Han-Yu; Wu, Shyuan-Guey; Tsui, Hung-Wei

    2017-04-21

    Stoichiometric displacement models have been widely used for understanding the adsorption mechanisms of solutes in chromatography systems. Such models are used for interpreting plots of solute retention factor versus concentrations of polar modifier in an inert solvent. However, these models often assume that dispersion forces are negligible and they are unable to account for solutes with significant aromatic interactions. In this study, a systematic investigation of the relationship between retention behavior and aromatic groups was performed using five simple aromatic molecules-benzene, naphthalene, mesitylene, durene, and toluene-with a commercially available amylose tris(3,5-dimethylphenylcarbamate)-based sorbent. The enthalpy changes of adsorption, determined from van't Hoff plots, were obtained separately in pure n-hexane and in pure isopropanol (IPA). In pure n-hexane, the solute adsorptions were driven by electrostatic interactions, favoring a T-shaped binding configuration (edge-to-face π-π interaction). The order of enthalpy change indicated the amount of effective T-shaped π-interactions. In pure IPA, solute adsorption was dominated by dispersion forces, favoring a sandwich binding configuration (face-to-face π-π interaction). The adsorption isotherms of toluene revealed that in pure IPA and in pure n-hexane, the isotherms were linear. The results suggested that the high solvent strength of IPA weakened the interactions between aromatic molecules. The retention behavior of the benzene, naphthalene, mesitylene, and durene as a function of IPA concentration was investigated. U-shaped retention curves were found for all aromatic solutes. A new retention model for monovalent aromatic solutes was developed for describing the U-shaped curves. Three key dimensionless groups were revealed to control the retention behavior. The models suggested that solvophobic interactions should be accounted for in the retention models used to investigate the retention

  20. A weighted random walk approximation to fractional Brownian motion

    OpenAIRE

    Lindstrøm, Tom

    2007-01-01

    We present a random walk approximation to fractional Brownian motion where the increments of the fractional random walk are defined as a weighted sum of the past increments of a Bernoulli random walk.

  1. A random walk approximation to fractional Brownian motion

    OpenAIRE

    Lindstrøm, Tom

    2007-01-01

    We present a random walk approximation to fractional Brownian motion where the increments of the fractional random walk are defined as a weighted sum of the past increments of a Bernoulli random walk.

  2. Small-Molecule Stabilization of the 14-3-3/Gab2 Protein-Protein Interaction (PPI) Interface.

    Science.gov (United States)

    Bier, David; Bartel, Maria; Sies, Katharina; Halbach, Sebastian; Higuchi, Yusuke; Haranosono, Yu; Brummer, Tilman; Kato, Nobuo; Ottmann, Christian

    2016-04-19

    Small-molecule modulation of protein-protein interactions (PPIs) is one of the most promising new areas in drug discovery. In the vast majority of cases only inhibition or disruption of PPIs is realized, whereas the complementary strategy of targeted stabilization of PPIs is clearly under-represented. Here, we report the example of a semi-synthetic natural product derivative--ISIR-005--that stabilizes the cancer-relevant interaction of the adaptor protein 14-3-3 and Gab2. The crystal structure of ISIR-005 in complex with 14-3-3 and the binding motif of Gab2 comprising two phosphorylation sites (Gab2pS210pT391) showed how the stabilizing molecule binds to the rim-of-the-interface of the protein complex. Only in the direct vicinity of 14-3-3/Gab2pT391 site is a pre-formed pocket occupied by ISIR-005; binding of the Gab2pS210 motif to 14-3-3 does not create an interface pocket suitable for the molecule. Accordingly, ISIR-005 only stabilizes the binding of the Gab2pT391 but not the Gab2pS210 site. This study represents structural and biochemical proof of the druggability of the 14-3-3/Gab2 PPI interface with important implications for the development of PPI stabilizers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Utilizing Biotinylated Proteins Expressed in Yeast to Visualize DNA–Protein Interactions at the Single-Molecule Level

    Directory of Open Access Journals (Sweden)

    Huijun Xue

    2017-10-01

    Full Text Available Much of our knowledge in conventional biochemistry has derived from bulk assays. However, many stochastic processes and transient intermediates are hidden when averaged over the ensemble. The powerful technique of single-molecule fluorescence microscopy has made great contributions to the understanding of life processes that are inaccessible when using traditional approaches. In single-molecule studies, quantum dots (Qdots have several unique advantages over other fluorescent probes, such as high brightness, extremely high photostability, and large Stokes shift, thus allowing long-time observation and improved signal-to-noise ratios. So far, however, there is no convenient way to label proteins purified from budding yeast with Qdots. Based on BirA–Avi and biotin–streptavidin systems, we have established a simple method to acquire a Qdot-labeled protein and visualize its interaction with DNA using total internal reflection fluorescence microscopy. For proof-of-concept, we chose replication protein A (RPA and origin recognition complex (ORC as the proteins of interest. Proteins were purified from budding yeast with high biotinylation efficiency and rapidly labeled with streptavidin-coated Qdots. Interactions between proteins and DNA were observed successfully at the single-molecule level.

  4. A novel paradigm for cell and molecule interaction ontology: from the CMM model to IMGT-ONTOLOGY

    Science.gov (United States)

    2010-01-01

    Background Biology is moving fast toward the virtuous circle of other disciplines: from data to quantitative modeling and back to data. Models are usually developed by mathematicians, physicists, and computer scientists to translate qualitative or semi-quantitative biological knowledge into a quantitative approach. To eliminate semantic confusion between biology and other disciplines, it is necessary to have a list of the most important and frequently used concepts coherently defined. Results We propose a novel paradigm for generating new concepts for an ontology, starting from model rather than developing a database. We apply that approach to generate concepts for cell and molecule interaction starting from an agent based model. This effort provides a solid infrastructure that is useful to overcome the semantic ambiguities that arise between biologists and mathematicians, physicists, and computer scientists, when they interact in a multidisciplinary field. Conclusions This effort represents the first attempt at linking molecule ontology with cell ontology, in IMGT-ONTOLOGY, the well established ontology in immunogenetics and immunoinformatics, and a paradigm for life science biology. With the increasing use of models in biology and medicine, the need to link different levels, from molecules to cells to tissues and organs, is increasingly important. PMID:20167082

  5. Xalpha-DVM investigation of double water molecule interactions with active sites of alpha- and beta-subunits of hemoglobin

    Science.gov (United States)

    Yuryeva, Elmira I.

    In this work, the results of Xalpha-discrete variation method calculations of the electronic structure and interatomic parameters of chemical bonding between iron (II) and oxygen molecule with and without extra electrons and protons in active site (AS) of alpha- and beta-subunits of oxyhemoglobin are presented. The Skulachev model of O2 molecule existing in respiration medium in the 2H2O form was used. The introduction of extra electrons does not change considerably the interaction of the iron atom with the O2 oxygen molecule, but strengthens the repulsion in the Fe bond N bonds. In this case, the estimated effective charge of the iron atom is +1.8/1.5e for AS of alpha-/beta-subunits of oxyhemoglobin, and the magnetic moment of iron atoms becomes zero. The deoxygenation effect of the AS of the alpha- and beta-subunits of oxyhemoglobin is due to the ability of extra protons to break down covalent attraction between the iron atom and the nearest oxygen atom and also to weakening of the repulsive component of the covalent Fe bond N interactions.

  6. Theoretical studies on CH+ ion molecule using configuration interaction method and its spectroscopic properties

    International Nuclear Information System (INIS)

    Machado, F.B.C.

    1985-01-01

    The use of the configuration (CI) method for the calculation of very accurate potential energy curves and dipole moment functions, and then their use in the comprehension of spectroscopic properties of diatomic molecules is presented. The spectroscopic properties of CH + and CD + such as: vibrational levels, spectroscopic constants, averaged dipole moments for all vibrational levels, radiative transition probabilities for emission and absorption, and radiative lifetimes are verificated. (M.J.C.) [pt

  7. Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions.

    Science.gov (United States)

    Bryan, Louise C; Weilandt, Daniel R; Bachmann, Andreas L; Kilic, Sinan; Lechner, Carolin C; Odermatt, Pascal D; Fantner, Georg E; Georgeon, Sandrine; Hantschel, Oliver; Hatzimanikatis, Vassily; Fierz, Beat

    2017-10-13

    Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling. We show that the three human HP1 isoforms are recruited and retained on chromatin by a dynamic exchange between histone PTM and DNA bound states. These interactions depend on local chromatin structure, the HP1 isoforms as well as on PTMs on HP1 itself. Of the HP1 isoforms, HP1α exhibits the longest residence times and fastest binding rates due to DNA interactions in addition to PTM binding. HP1α phosphorylation further increases chromatin retention through strengthening of multivalency while reducing DNA binding. As DNA binding in combination with specific PTM recognition is found in many chromatin effectors, we propose a general dynamic capture mechanism for effector recruitment. Multiple weak protein and DNA interactions result in a multivalent interaction network that targets effectors to a specific chromatin modification state, where their activity is required. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. I.I. Rabi in Atomic, Molecular & Optical Physics Prize Talk: Strongly Interacting Fermi Gases of Atoms and Molecules

    Science.gov (United States)

    Zwierlein, Martin

    2017-04-01

    Strongly interacting fermions govern physics at all length scales, from nuclear matter to modern electronic materials and neutron stars. The interplay of the Pauli principle with strong interactions can give rise to exotic properties that we do not understand even at a qualitative level. In recent years, ultracold Fermi gases of atoms have emerged as a new type of strongly interacting fermionic matter that can be created and studied in the laboratory with exquisite control. Feshbach resonances allow for unitarity limited interactions, leading to scale invariance, universal thermodynamics and a superfluid phase transition already at 17 Trapped in optical lattices, fermionic atoms realize the Fermi-Hubbard model, believed to capture the essence of cuprate high-temperature superconductors. Here, a microscope allows for single-atom, single-site resolved detection of density and spin correlations, revealing the Pauli hole as well as anti-ferromagnetic and doublon-hole correlations. Novel states of matter are predicted for fermions interacting via long-range dipolar interactions. As an intriguing candidate we created stable fermionic molecules of NaK at ultralow temperatures featuring large dipole moments and second-long spin coherence times. In some of the above examples the experiment outperformed the most advanced computer simulations of many-fermion systems, giving hope for a new level of understanding of strongly interacting fermions.

  9. Fast orthogonal transforms and generation of Brownian paths.

    Science.gov (United States)

    Leobacher, Gunther

    2012-04-01

    We present a number of fast constructions of discrete Brownian paths that can be used as alternatives to principal component analysis and Brownian bridge for stratified Monte Carlo and quasi-Monte Carlo. By fast we mean that a path of length [Formula: see text] can be generated in [Formula: see text] floating point operations. We highlight some of the connections between the different constructions and we provide some numerical examples.

  10. Estimation of the global regularity of a multifractional Brownian motion

    DEFF Research Database (Denmark)

    Lebovits, Joachim; Podolskij, Mark

    This paper presents a new estimator of the global regularity index of a multifractional Brownian motion. Our estimation method is based upon a ratio statistic, which compares the realized global quadratic variation of a multifractional Brownian motion at two different frequencies. We show that a ...... that a logarithmic transformation of this statistic converges in probability to the minimum of the Hurst functional parameter, which is, under weak assumptions, identical to the global regularity index of the path....

  11. Estimation of the global regularity of a multifractional Brownian motion

    OpenAIRE

    Lebovits, Joachim; Podolskij, Mark

    2016-01-01

    This paper presents a new estimator of the global regularity index of a multifractional Brownian motion. Our estimation method is based upon a ratio statistic, which compares the realized global quadratic variation of a multifractional Brownian motion at two different frequencies. We show that a logarithmic transformation of this statistic converges in probability to the minimum of the Hurst functional parameter, which is, under weak assumptions, identical to the global regularity index of th...

  12. Critical evaluation of dipolar, acid-base and charge interactions I. Electron displacement within and between molecules, liquids and semiconductors.

    Science.gov (United States)

    Rosenholm, Jarl B

    2017-09-01

    Specific dipolar, acid-base and charge interactions involve electron displacements. For atoms, single bonds and molecules electron displacement is characterized by electronic potential, absolute hardness, electronegativity and electron gap. In addition, dissociation, bonding, atomization, formation, ionization, affinity and lattice enthalpies are required to quantify the electron displacement in solids. Semiconductors are characterized by valence and conduction band energies, electron gaps and average Fermi energies which in turn determine Galvani potentials of the bulk, space charge layer and surface states. Electron displacement due to interaction between (probe) molecules, liquids and solids are characterized by parameters such as Hamaker constant, solubility parameter, exchange energy density, surface tension, work of adhesion and immersion. They are determined from permittivity, refractive index, enthalpy of vaporization, molar volume, surface pressure and contact angle. Moreover, acidic and basic probes may form adducts which are adsorbed on target substrates in order to establish an indirect measure of polarity, acidity, basicity or hydrogen bonding. Acidic acceptor numbers (AN), basic donor numbers (DN), acidic and basic "electrostatic" (E) and "covalent" (C) parameters determined by enthalpy of adduct formation are considered as general acid-base scales. However, the formal grounds for assignments as dispersive, Lifshitz-van der Waals, polar, acid, base and hydrogen bond interactions are inconsistent. Although correlations are found no of the parameters are mutually fully compatible and moreover the enthalpies of acid-base interaction do not correspond to free energies. In this review the foundations of different acid-base parameters relating to electron displacement within and between (probe) molecules, liquids and (semiconducting) solids are thoroughly investigated and their mutual relationships are evaluated. Copyright © 2017 Elsevier B.V. All rights

  13. Gp63-like molecules in Phytomonas serpens: possible role in the insect interaction.

    Science.gov (United States)

    d'Avila-Levy, Claudia M; Santos, Lívia O; Marinho, Fernanda A; Dias, Felipe A; Lopes, Angela H; Santos, André L S; Branquinha, Marta H

    2006-06-01

    In this study, we demonstrated that metallopeptidase inhibitors (EDTA, EGTA, and 1,10-phenanthroline) were able to arrest Phytomonas serpens growth in distinct patterns. This parasite released exclusively metallopeptidases to the extracellular environment, whereas in cellular extracts only cysteine peptidases were detected. In addition, an extracellular polypeptide of 60 kDa reacted in Western blotting probed with polyclonal antibody raised against gp63 of Leishmania amazonensis. In the cellular parasite extract, this antibody recognized bands migrating at 63 and 52 kDa, which partitioned on both aqueous and membrane-rich fractions. Flow cytometry and fluorescence microscopy analyses showed that the gp63-like molecules have a surface location. Moreover, phospholipase C (PLC)-treated parasites reduced the number of gp63-positive cells. The anti-cross-reacting determinant (CRD) and anti-gp63 antibodies recognized the 60-kDa band in the supernatant from PLC-treated cells, suggesting that this protein is glycosylphosphatidylinositol-anchored to the plasma membrane. This is the first report on the presence of gp63-like molecules in members of the Phytomonas genus. The pretreatment of the parasites with anti-gp63 antibody significantly diminished their adhesion index to explanted salivary glands of the phytophagous insect Oncopeltus fasciatus, suggesting a potential involvement of the gp63-like molecules in the adhesive process of this plant trypanosomatid.

  14. Interaction of an immunodominant epitope with Ia molecules in T-cell activation

    DEFF Research Database (Denmark)

    Adorini, L; Sette, A; Buus, S

    1988-01-01

    The amino acid sequence corresponding to residues 107-116 of hen egg-white lysozyme (HEL) has been identified as containing an immunodominant T-cell epitope recognized in association with the I-Ed molecule. The immunodominance of this epitope in HEL-primed H-2d mice was demonstrated by analysis...... of the T-cell proliferative response induced by synthetic peptides covering almost the entire HEL sequence. All the T-cell hybridomas from H-2d mice analyzed recognize the HEL sequence 107-116 in association with the I-Ed molecule. Correlating with the restriction of T-cell recognition, HEL-(105......-120)-peptide binds to I-Ed but not to I-Ad molecules. Conservative or semiconservative substitutions at positions 113 (Asn----Lys), 114 (Arg----His), or 115 (Cys----Ala) abrogate the ability of HEL-(105-120) to activate T cells. Substitutions at residues 113 and 115 affect T-cell recognition...

  15. Modulation of the homophilic interaction between the first and second Ig modules of neural cell adhesion molecule by heparin

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Rudenko, Olga; Kiselyov, V.

    2005-01-01

    The second Ig module (IgII) of the neural cell adhesion molecule (NCAM) is known to bind to the first Ig module (IgI) of NCAM (so-called homophilic binding) and to interact with heparan sulfate and chondroitin sulfate glycoconjugates. We here show by NMR that the heparin and chondroitin sulfate......-binding sites (HBS and CBS, respectively) in IgII coincide, and that this site overlaps with the homophilic binding site. Using NMR and surface plasmon resonance (SPR) analyses we demonstrate that interaction between IgII and heparin indeed interferes with the homophilic interaction between IgI and Ig......II. Accordingly, we show that treatment of cerebellar granule neurons (CGNs) with heparin inhibits NCAM-mediated outgrowth. In contrast, treatment with heparinase III or chondroitinase ABC abrogates NCAM-mediated neurite outgrowth in CGNs emphasizing the importance of the presence of heparan/chondroitin sulfates...

  16. Small Molecule Binding, Docking, and Characterization of the Interaction between Pth1 and Peptidyl-tRNA

    Directory of Open Access Journals (Sweden)

    Mary C. Hames

    2013-11-01

    Full Text Available Bacterial Pth1 is essential for viability. Pth1 cleaves the ester bond between the peptide and nucleotide of peptidyl-tRNA generated from aborted translation, expression of mini-genes, and short ORFs. We have determined the shape of the Pth1:peptidyl-tRNA complex using small angle neutron scattering. Binding of piperonylpiperazine, a small molecule constituent of a combinatorial synthetic library common to most compounds with inhibitory activity, was mapped to Pth1 via NMR spectroscopy. We also report computational docking results, modeling piperonylpiperazine binding based on chemical shift perturbation mapping. Overall these studies promote Pth1 as a novel antibiotic target, contribute to understanding how Pth1 interacts with its substrate, advance the current model for cleavage, and demonstrate feasibility of small molecule inhibition.

  17. A Mechanical Model of Brownian Motion for One Massive Particle Including Slow Light Particles

    Science.gov (United States)

    Liang, Song

    2018-01-01

    We provide a connection between Brownian motion and a classical mechanical system. Precisely, we consider a system of one massive particle interacting with an ideal gas, evolved according to non-random mechanical principles, via interaction potentials, without any assumption requiring that the initial velocities of the environmental particles should be restricted to be "fast enough". We prove the convergence of the (position, velocity)-process of the massive particle under a certain scaling limit, such that the mass of the environmental particles converges to 0 while the density and the velocities of them go to infinity, and give the precise expression of the limiting process, a diffusion process.

  18. Chemometric analysis reveals links in the formation of fragrant bio-molecules during agarwood (Aquilaria malaccensis) and fungal interactions.

    Science.gov (United States)

    Sen, Supriyo; Dehingia, Madhusmita; Talukdar, Narayan Chandra; Khan, Mojibur

    2017-03-14

    Fragrant agarwood, arguably the costliest wood in the world, is formed by plant-fungal interactions in Aquilaria spp. However, very little is known about this fragrant outcome of interaction. Therefore, mimicking the ancient traditions of agarwood production in Assam (Northeast India), a chemometric assessment of the agarwood-fungus interaction was made by chemical profiling (GC-MS) coupled with statistical analysis (principal component, correlation network analysis) across three platforms, viz. callus, juvenile plants and resinous wood-chips with an associated Fusarium. In the study of callus-fungus interaction, increased accumulation of key aroma compounds such as pentatriacontane {fold change (log2FC) = 3.47)}, 17-pentatriacontene (log2FC = 2.95), tetradecane, 2-methyl- (log2FC = 1.10) over callus and activation of pathways related to defense and secondary metabolism indicated links to aroma production. Study on fungal interactions in juvenile plants and resinous wood-chips indicated formation of terpenoid precursors (e.g. farnesol, geranylgeraniol acetate) and agarwood sesquiterpenes (e.g. agarospirol, γ-eudesmol). Correlation network analysis revealed the possible regulation of sesquiterpene biosynthesis involving squalene. Also a direct role of fungus in aroma (e.g. dodecane, 4-methyl-, tetracosane) was highlighted. Appearance of fragrant molecules unknown to agarwood during interaction featured as a new possibility for future research.

  19. High-field Solution NMR Spectroscopy as a Tool for Assessing Protein Interactions with Small Molecule Ligands

    Science.gov (United States)

    Skinner, Andria L.; Laurence, Jennifer S.

    2013-01-01

    The ability of a small molecule to bind and modify the activity of a protein target at a specific site greatly impacts the success of drugs in the pharmaceutical industry. One of the most important tools for evaluating these interactions has been high-field solution NMR because of its unique ability to examine even weak protein-drug interactions at high resolution. NMR can be used to evaluate the structural, thermodynamic and kinetic aspects of a binding reaction. The basis of NMR screening experiments is that binding causes a perturbation in the physical properties of both molecules. Unique properties of small and macromolecules allow selective detection of either the protein target or ligand, even in a mixture of compounds. This review outlines current methodologies for assessing protein-ligand interactions from the perspectives of the protein target and ligand and delineates the fundamental principles for understanding NMR approaches in drug research. Advances in instrumentation, pulse sequences, isotopic labeling strategies, and the development of competition experiments support the study of higher molecular weight protein targets, facilitate higher-throughput and expand the range of binding affinities that can be evaluated, enhancing the utility of NMR for identifying and characterizing potential therapeutics to druggable protein targets. PMID:18351634

  20. Regulation of drug-metabolizing enzymes in infectious and inflammatory disease: implications for biologics-small molecule drug interactions.

    Science.gov (United States)

    Mallick, Pankajini; Taneja, Guncha; Moorthy, Bhagavatula; Ghose, Romi

    2017-06-01

    Drug-metabolizing enzymes (DMEs) are primarily down-regulated during infectious and inflammatory diseases, leading to disruption in the metabolism of small molecule drugs (smds), which are increasingly being prescribed therapeutically in combination with biologics for a number of chronic diseases. The biologics may exert pro- or anti-inflammatory effect, which may in turn affect the expression/activity of DMEs. Thus, patients with infectious/inflammatory diseases undergoing biologic/smd treatment can have complex changes in DMEs due to combined effects of the disease and treatment. Areas covered: We will discuss clinical biologics-SMD interaction and regulation of DMEs during infection and inflammatory diseases. Mechanistic studies will be discussed and consequences on biologic-small molecule combination therapy on disease outcome due to changes in drug metabolism will be highlighted. Expert opinion: The involvement of immunomodulatory mediators in biologic-SMDs is well known. Regulatory guidelines recommend appropriate in vitro or in vivo assessments for possible interactions. The role of cytokines in biologic-SMDs has been documented. However, the mechanisms of drug-drug interactions is much more complex, and is probably multi-factorial. Studies aimed at understanding the mechanism by which biologics effect the DMEs during inflammation/infection are clinically important.

  1. From Brownian motion to power of fluctuations

    Directory of Open Access Journals (Sweden)

    B. Berche

    2012-12-01

    Full Text Available The year 2012 marks the 140th birth anniversary of Marian Smoluchowski (28.05.1872-5.09.1917, a man who "made ground-breaking contribution to the theory of Brownian motion, the theory of sedimentation, the statistical nature of the Second Law, the theory and practice of density fluctuations (critical opalescence. During his final years of scientific creativity his pioneering theory of coagulation and diffusion-limited reaction rate appeared. These outstanding achievements present true gems which dominate the description of soft matter physics and chemical physics as well as the related areas up till now!" This quotation was taken from the lecture by Peter Hanggi given at international conference Statistical Physics: Modern Trends and Applications that took place in Lviv, Ukraine on July 3-6, 2012 (see conference web-page for more details and was dedicated to the commemoration of Smoluchowski's work. This and forthcoming issues of the Condensed Matter Physics contain papers presented at this conference.

  2. Shear thinning in non-Brownian suspensions.

    Science.gov (United States)

    Chatté, Guillaume; Comtet, Jean; Niguès, Antoine; Bocquet, Lydéric; Siria, Alessandro; Ducouret, Guylaine; Lequeux, François; Lenoir, Nicolas; Ovarlez, Guillaume; Colin, Annie

    2018-02-14

    We study the flow of suspensions of non-Brownian particles dispersed into a Newtonian solvent. Combining capillary rheometry and conventional rheometry, we evidence a succession of two shear thinning regimes separated by a shear thickening one. Through X-ray radiography measurements, we show that during each of those regimes, the flow remains homogeneous and does not involve particle migration. Using a quartz-tuning fork based atomic force microscope, we measure the repulsive force profile and the microscopic friction coefficient μ between two particles immersed into the solvent, as a function of normal load. Coupling measurements from those three techniques, we propose that (1) the first shear-thinning regime at low shear rates occurs for a lubricated rheology and can be interpreted as a decrease of the effective volume fraction under increasing particle pressures, due to short-ranged repulsive forces and (2) the second shear thinning regime after the shear-thickening transition occurs for a frictional rheology and can be interpreted as stemming from a decrease of the microscopic friction coefficient at large normal load.

  3. Effects of ionizing radiation on cell-matrix interactions at the single molecule level

    Energy Technology Data Exchange (ETDEWEB)

    Lauer, Florian

    2015-04-20

    Single molecule microscopy is a technology that allows for accurate assessment of the location and motion of single fluorescent molecules, even in the context of observations on living biological samples. In the present thesis, a flexible analysis tool for single molecule data as obtained in biological experiments was established. The development of a tool to faithfully detect and localize diffraction-limited images of individual fluorescent probes was necessary since data acquired under cell cultivation conditions that account for a three-dimensional microenvironment as experienced physiologically by cells in native tissue poses a challenge not faced ordinarily. After design, implementation, quantitative tests using simulations for comparisons and verification, and evaluation of the different steps of the analysis procedure including local background estimation, local noise estimation, de-noising approaches, detection, localization, and post-processing, analysis capabilities were utilized to evaluate the impact of x-ray irradiation on the plasma membrane architecture of U2OS human osteosarcoma cells as assessed by tracking individual fluorescent lipid-mimetic dye molecules diffusing in the outer membrane leaflet. It was shown that lateral diffusion in the plasma membrane is well described as two-phase anomalous subdiffusion and presence of 3D extracellular matrix leads to lower anomalous exponents of the fast fraction in comparison to monolayer cell culture. Interestingly, even high single-dose (25 Gy) treatments known to induce membrane-mediated apoptosis in tumor microvessel endothelium via membrane viscosity enhancing ceramide generation were not observed to alter membrane architecture in U2OS cells which can be related to amplifying, feedback-driven redox-signaling in the endothelium absent in U2OS. In summary, the sensitive and accurate framework developed in this thesis to assess minute changes of plasma membrane located dynamic processes did not uncover a

  4. Phase transition in non-brownian fiber suspensions

    Science.gov (United States)

    Franceschini, Alexandre; Filippidi, Emmanouella; Guazzelli, Elizabeth; Pine, David

    2012-11-01

    The simple shear of a suspension of fibers tends to align them with the flow direction. We previously reported that the oscillatory shear of neutrally buoyant non-Brownian fibers align them with the vorticity (Franceschini A. et al. PRL, 2011). We interpreted this phenomenon as the minimization of a ``corrected volume fraction'' defined as a function of the strain amplitude, the average orientation and the volume fraction. Below a critical value of this parameter, the system becomes fully reversible after a few periods. Above it, fluctuations remain and the fibers align with the vorticity, subsequently reducing the value of this corrected volume fraction. We present here the collective behavior of fibers constrained at the liquid-air interface. By pinning the liquid on the wall of a Couette cell, we can have a flat interface. By modifying the surface of the fibers, we get rid of most of surface tension mediated fiber-fiber interactions. In this 2D configuration we can measure spatial correlations, as well as the position and orientation of every fiber at each shear cycle. We similarly define a ``corrected surface fraction'' and see how this parameter help us understand the difference between the surface behavior and the suspension behavior. This work was supported by the NSF through the NYU MRSEC, Award DMR:0820341. Additional support was provided by a Lavoisier Fellowship (AF) and from the Onassis Foundation (EF).

  5. Brownian dynamics of wall tethered polymers in shear flow

    Science.gov (United States)

    Lin, Tiras Y.; Saadat, Amir; Kushwaha, Amit; Shaqfeh, Eric S. G.

    2017-11-01

    The dynamics of a wall tethered polymer in shear flow is studied using Brownian dynamics. Simulations are performed with bead-spring chains, and the effect of hydrodynamic interactions (HI) is incorporated through Blake's tensor with a finite size bead correction. We characterize the configuration of the polymer as a function of the Weissenberg number by investigating the regions the polymer explores in both the flow-gradient and flow-vorticity planes. The fractional extension in the flow direction, the width in the vorticity direction, and the thickness in the gradient direction are reported as well, and these quantities are found to compare favorably with the experimental data of the literature. The cyclic motion of the polymer is demonstrated through analysis of the mean velocity field of the end bead. We characterize the collision process of each bead with the wall as a Poisson process and extract an average wall collision rate, which in general varies along the backbone of the chain. The inclusion of HI with the wall for a tethered polymer is found to reduce the average wall collision rate. We anticipate that results from this work will be directly applicable to, e.g., the design of polymer brushes or the use of DNA for making nanowires in molecular electronics. T.Y.L. is supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.

  6. Bose polaron as an instance of quantum Brownian motion

    Directory of Open Access Journals (Sweden)

    Aniello Lampo

    2017-09-01

    Full Text Available We study the dynamics of a quantum impurity immersed in a Bose-Einstein condensate as an open quantum system in the framework of the quantum Brownian motion model. We derive a generalized Langevin equation for the position of the impurity. The Langevin equation is an integrodifferential equation that contains a memory kernel and is driven by a colored noise. These result from considering the environment as given by the degrees of freedom of the quantum gas, and thus depend on its parameters, e.g. interaction strength between the bosons, temperature, etc. We study the role of the memory on the dynamics of the impurity. When the impurity is untrapped, we find that it exhibits a super-diffusive behavior at long times. We find that back-flow in energy between the environment and the impurity occurs during evolution. When the particle is trapped, we calculate the variance of the position and momentum to determine how they compare with the Heisenberg limit. One important result of this paper is that we find position squeezing for the trapped impurity at long times. We determine the regime of validity of our model and the parameters in which these effects can be observed in realistic experiments.

  7. Cross Talk between H2O2 and Interacting Signal Molecules under Plant Stress Response

    Science.gov (United States)

    Saxena, Ina; Srikanth, Sandhya; Chen, Zhong

    2016-01-01

    It is well established that oxidative stress is an important cause of cellular damage. During stress conditions, plants have evolved regulatory mechanisms to adapt to various environmental stresses. One of the consequences of stress is an increase in the cellular concentration of reactive oxygen species, which is subsequently converted to H2O2. H2O2 is continuously produced as the byproduct of oxidative plant aerobic metabolism. Organelles with a high oxidizing metabolic activity or with an intense rate of electron flow, such as chloroplasts, mitochondria, or peroxisomes are major sources of H2O2 production. H2O2 acts as a versatile molecule because of its dual role in cells. Under normal conditions, H2O2 immerges as an important factor during many biological processes. It has been established that it acts as a secondary messenger in signal transduction networks. In this review, we discuss potential roles of H2O2 and other signaling molecules during various stress responses. PMID:27200043

  8. Stabilization of the Central Part of Tropomyosin Molecule Alters the Ca2+-sensitivity of Actin-Myosin Interaction

    OpenAIRE

    Shchepkin, D.V.; Matyushenko, A. M.; Kopylova, G. V.; Artemova, N. V.; Bershitsky, S. Y.; Tsaturyan, A. K.; Levitsky, D. I.

    2013-01-01

    We show that the mutations D137L and G126R, which stabilize the central part of the tropomyosin (Tm) molecule, increase both the maximal sliding velocity of the regulated actin filaments in the in vitro motility assay at high Са 2+ concentrations and the Са 2+-sensitivity of the actin-myosin interaction underlying this sliding. Based on an analysis of the recently published data on the structure of the actin–Tm–myosin complex, we suppose that the physiological effects of these mutations in Tm...

  9. Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches.

    Science.gov (United States)

    Ma, Songling; Choi, Jiwon; Jin, Xuemei; Kim, Hyun-Yi; Yun, Ji-Hye; Lee, Weontae; Choi, Kang-Yell; No, Kyoung Tai

    2018-04-07

    The Wnt/β-catenin signaling pathway plays a significant role in the control of osteoblastogenesis and bone formation. CXXC finger protein 5 (CXXC5) has been recently identified as a negative feedback regulator of osteoblast differentiation through a specific interaction with Dishevelled (Dvl) protein. It was reported that targeting the Dvl-CXXC5 interaction could be a novel anabolic therapeutic target for osteoporosis. In this study, complex structure of Dvl PDZ domain and CXXC5 peptide was simulated with molecular dynamics (MD). Based on the structural analysis of binding modes of MD-simulated Dvl PDZ domain with CXXC5 peptide and crystal Dvl PDZ domain with synthetic peptide-ligands, we generated two different pharmacophore models and applied pharmacophore-based virtual screening to discover potent inhibitors of the Dvl-CXXC5 interaction for the anabolic therapy of osteoporosis. Analysis of 16 compounds selected by means of a virtual screening protocol yielded four compounds that effectively disrupted the Dvl-CXXC5 interaction in the fluorescence polarization assay. Potential compounds were validated by fluorescence spectroscopy and nuclear magnetic resonance. We successfully identified a highly potent inhibitor, BMD4722, which directly binds to the Dvl PDZ domain and disrupts the Dvl-CXXC5 interaction. Overall, CXXC5-Dvl PDZ domain complex based pharmacophore combined with various traditional and simple computational methods is a promising approach for the development of modulators targeting the Dvl-CXXC5 interaction, and the potent inhibitor BMD4722 could serve as a starting point to discover or design more potent and specific the Dvl-CXXC5 interaction disruptors.

  10. Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy.

    Science.gov (United States)

    Lee, Jieun; Ju, Soomi; Kim, In Tae; Jung, Sun-Hwa; Min, Sun-Joon; Kim, Chulki; Sim, Sang Jun; Kim, Sang Kyung

    2015-12-04

    Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction.

  11. Cell-based protein stabilization assays for the detection of interactions between small-molecule inhibitors and BRD4.

    Science.gov (United States)

    Schulze, Jessica; Moosmayer, Dieter; Weiske, Joerg; Fernández-Montalván, Amaury; Herbst, Christopher; Jung, Marie; Haendler, Bernard; Bader, Benjamin

    2015-02-01

    Bromodomain protein 4 (BRD4), a member of the bromodomain and extra-terminal (BET) protein family, acts as a central element in transcriptional elongation and plays essential roles in cell proliferation. Inhibition of BRD4 binding to acetylated histone tails via its two bromodomains, BD1 and BD2, with small-molecule inhibitors has been shown to be a valid strategy to prevent cancer growth. We have evaluated and established two novel assays that quantify the interaction of transfected BRD4 BD1 with chemical inhibitors inside cultured cells. Both methods are based on the principle of ligand-induced protein stabilization by which the binding of a small-molecule inhibitor stabilizes intracellular BRD4 BD1 and protects it from proteolytic degradation. We demonstrate the universal character of this principle by using two orthogonal, highly sensitive detection technologies for the quantification of BRD4 BD1 levels in cellular lysates: enzyme fragment complementation and time-resolved fluorescence resonance energy transfer (TR-FRET). Upon optimization of both assays to a miniaturized high-throughput format, the methods were validated by testing a set of small-molecule BET inhibitors and comparing the results with those from a cell-free binding assay and a biophysical thermal shift assay. In addition, point mutations were introduced into BRD4 BD1, and the corresponding mutants were characterized in the TR-FRET stabilization assay. © 2014 Society for Laboratory Automation and Screening.

  12. On the interaction of guest molecules with Co-MOF-74: A Vis/NIR and Raman approach.

    Science.gov (United States)

    Strauss, Ina; Mundstock, Alexander; Hinrichs, Dominik; Himstedt, Rasmus; Knebel, Alexander; Reinhardt, Carsten; Dorfs, Dirk; Caro, Jürgen

    2018-03-13

    Co-MOF-74 rod like crystals with a length of several hundred micrometers have been synthesized via a solvothermal procedure and their interaction with different gases has been evaluated in view of selective gas sensing. We show strongly anisotropic absorption behaviour of the Co-MOF-74 crystals when illuminated with polarized light. This study then addresses the interactions of guests (CO2, propane, propene, Ar, MeOH, H2O) with Co-MOF-74, studied by various spectroscopic techniques. Via Vis/NIR measurements, peak shifts of Co-MOF-74 depending on the interaction with the guest molecules were observed and distinguished. In the visible as well as in the near infrared region, the maximum absorbance is shifted selectively corresponding to the intensity of the CoII-guest interaction. Even propene and propane could be distinguished at room temperature according to their different interactions with Co-MOF-74. Furthermore, we used Raman spectroscopy to detect a modified vibrational behaviour of Co-MOF-74 upon gas adsorption. We show that the adsorption of H2O leads to a characteristic shift of the peak maxima in the Raman spectra. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Interaction of mineral surfaces with simple organic molecules by diffuse reflectance IR spectroscopy (DRIFT)

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Joan E.; Kelley, Michael J.

    2008-06-01

    Diffuse reflectance Fourier-transform infrared spectroscopy (DRIFTS) was used to characterize multi-layers of lysine, glutamic acid and salicylic acid on -alumina and kaolinite surfaces. The results agreed well with those previously obtained by ATR-IR in aqueous media where available, indicating that DRIFT may be regarded as effectively an in-situ spectroscopy for these materials. In the case of salicylic acid adsorption onto γ-alumina, DRIFTS was used to identify monolayer coverage and to detect molecules down to coverage of 3% of a monolayer. The spectroscopic results as to coverage were confirmed by analysis of the solutions used for treatment. The spectra obtained allowed identification of changes in the bonding environment with increasing surface coverage. DRIFTS, offers several advantages in terms of materials, experimental technique and data treatment, motivating further investigations.

  14. Studying the molecular mechanisms of radiation damage : low-energy electron interactions with biomolecules and medically relevant molecules

    International Nuclear Information System (INIS)

    Tanzer, K.

    2015-01-01

    Since it was discovered in the year 2000 that secondary electrons with energies below 20 eV, which are the most abundant secondary species produced upon the interaction of ionizing radiation with biological tissue, can induce severe damages in the DNA such as single and double strand breaks, the interest for the study of the interaction of electrons with essential molecules of the human body has grown immensely. Double strand breaks can lead to cancer and are therefore a substantial threat to human health, however, the radiation research community is not sure how these strand breaks are formed upon interaction with ionizing radiation. The fact that even electrons with energies well below the ionization threshold can induce great damage in biological molecules via a resonant process called dissociative electron attachment (DEA), has even furthered the interest in these electron interactions, as it was shown to be a very efficient decomposition mechanism. A variety of studies, such as DEA studies to components of the DNA, for example, have been undertaken so far to shed more light on the role electrons play in the radiation damage of biomolecules. In this thesis two nucleobases, adenine and hypoxanthine, have been studied by observing their response towards low-energy electrons. It has been found that these nucleobases behave in a similar manner upon low-energy electron interaction, as do other nucleobases, that have been studied previously. The loss of hydrogen is suspected to act as a precursor for the decomposition of the DNA and the nucleobases can also undergo ring cleavage, which will induce substantial damage in the DNA. Furthermore, the search for improved and more efficient methods for the treatment of cancer is as important as ever, considering the ever-rising number of cancer deaths. Radiotherapy has proven to be one of the best treatments for tumors, but was found to be ineffective in hypoxic - oxygen deprived - tumors. Compounds called radiosensitizers

  15. Exploring the Interaction of Ruthenium(II) Polypyridyl Complexes with DNA Using Single-Molecule Techniques†

    Science.gov (United States)

    Mihailovic, Aleksandra; Vladescu, Ioana; McCauley, Micah; Ly, Elaine; Williams, Mark C.; Spain, Eileen M.; Nuñez, Megan E.

    2008-01-01

    Here we explore DNA binding by a family of ruthenium(II) polypyridyl complexes using an atomic force microscope (AFM) and optical tweezers. We demonstrate using AFM that Ru(bpy)2dppz2+ intercalates into DNA (Kb= 1.5 × 105 M−1), as does its close relative Ru(bpy)2dppx2+ (Kb= 1.5 × 105 M−1). However, intercalation by Ru(phen)32+ and other Ru(II) complexes with Kb's lower than Ru(bpy)2dppz2+ are difficult to determine using AFM because of competing aggregation and surface-binding phenomena. At the high Ru(II) concentrations required to evaluate intercalation, most of the DNA strands acquire a twisted, curled conformation that is impossible to measure accurately. The condensation of DNA on mica in the presence of polycations is well known, but it clearly precludes the accurate assessment by AFM of DNA intercalation by most Ru(II) complexes, though not by ethidium bromide and other monovalent intercalators. When stretching individual DNA molecules using optical tweezers the same limitation on high metal concentration does not exist. Using optical tweezers we show that Ru(phen)2dppz2+ intercalates avidly (Kb = 3.2 × 106 M−1) while Ru(bpy)32+ does not intercalate, even at micromolar ruthenium concentrations. Ru(phen)32+ is shown to intercalate weakly, i.e. at micromolar concentrations (Kb= 8.8 × 103 M−1). The distinct differences in DNA stretching behavior between Ru(phen)32+ and Ru(bpy)32+ clearly illustrate that intercalation can be distinguished from groove binding by pulling the DNA with optical tweezers. Our results demonstrate both the benefits and challenges of two single-molecule methods in exploring DNA binding, and help to elucidate the mode of binding of Ru(phen)32+. PMID:16649785

  16. Localization of CD9 Molecule on Bull Spermatozoa: Its Involvement in the Sperm-Egg Interaction.

    Science.gov (United States)

    Antalíková, J; Jankovičová, J; Simon, M; Cupperová, P; Michalková, K; Horovská, Ľ

    2015-06-01

    Tetraspanin CD9 is one of the egg membrane proteins known to be essential in fertilization process. The presence and localization of CD9 molecule in spermatozoa and its possible function in reproduction are still unclear. In our study, we describe the localization of CD9 on bull spermatozoa. In the immunofluorescence assay, the positive signal has been observed in the high proportion of sperm cells as a fine grains either on the apical part or through the entire anterior region of sperm head. CD9 recognized by monoclonal antibody IVA-50 was detected on freshly ejaculated (83.4 ± 3.7%) and frozen-thawed (84.3 ± 2.3%) sperm. The same reaction pattern was observed on sperm capacitated for 1 h, 2 h, 3 h and 4 h (83.6 ± 2.0%; 84.0 ± 1.5%; 85.7 ± 0.8%; 77.5 ± 10.8%). The presence of CD9 exclusively on plasma membrane of the bovine sperm has been detected by Western blot analysis of the protein fractions after the discontinuous sucrose gradient fractionation of the bull sperm. Moreover, probable role of the sperm CD9 molecule in fertilization process of cattle has been suggested as sperm treatment with anti-CD9 antibody significantly reduced (by 25%, p ≤ 0.001) the number of fertilized oocytes compared to control group in fertilization assay in vitro. © 2015 Blackwell Verlag GmbH.

  17. Effect of van der Waals interaction on energetics and transport properties of a single anthracene molecule adsorbed or confined inside a carbon nanotube

    Science.gov (United States)

    Debbichi, L.; Dappe, Y. J.; Alouani, M.

    2012-01-01

    The energetics and transport properties of a single aromatic molecule (C14H10) in interaction with a metallic single-walled carbon nanotube (SWCNT) have been studied using state-of-the-art density functional calculations. In both adsorption and encapsulation configurations, we show that the fundamental importance of the weak van der Waals (vdW) interactions is to stabilize the position of the molecule. These interactions have been treated through the ab initio linear combination of atomic orbitals (LCAO-S2) method including the vdW weak interactions. Moreover, we show that the electric conductance of the SWCNT, calculated within a nonequilibrium Green's-function formalism, is very sensitive to the position of the molecule with respect to the nanotube. The change of the conductance is explained in terms of charge transfer strength between the nanotube and the molecule.

  18. The special theory of Brownian relativity: equivalence principle for dynamic and static random paths and uncertainty relation for diffusion.

    Science.gov (United States)

    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.

  19. Stabilization of the Central Part of Tropomyosin Molecule Alters the Ca2+-sensitivity of Actin-Myosin Interaction.

    Science.gov (United States)

    Shchepkin, D V; Matyushenko, A M; Kopylova, G V; Artemova, N V; Bershitsky, S Y; Tsaturyan, A K; Levitsky, D I

    2013-07-01

    We show that the mutations D137L and G126R, which stabilize the central part of the tropomyosin (Tm) molecule, increase both the maximal sliding velocity of the regulated actin filaments in the in vitro motility assay at high Са(2+) concentrations and the Са(2+)-sensitivity of the actin-myosin interaction underlying this sliding. Based on an analysis of the recently published data on the structure of the actin-Tm-myosin complex, we suppose that the physiological effects of these mutations in Tm can be accounted for by their influence on the interactions between the central part of Tm and certain sites of the myosin head.

  20. Microbial volatiles: Small molecules with an important role in intra- and inter-kingdom interactions

    NARCIS (Netherlands)

    Schulz-Bohm, K.; Martín-Sánchez, L.; Garbeva, P.V.

    2017-01-01

    During the last decades, research on the function of volatile organic compounds focused primarily on the interactions between plants and insects. However, microorganisms can also release a plethora of volatiles and it appears that microbial volatile organic compounds (mVOCs) can play an important

  1. Infrared studies of astronomically relevant metallic clusters and their interactions with simple molecules

    NARCIS (Netherlands)

    Kiawi, D.M.

    2016-01-01

    The work presented in this thesis aims at: a) providing fundamental knowledge on the interactions of simple ligands with metal clusters relevant to astronomical and (bio-) catalytical processes, b) providing a benchmark that can be used to test current and future DFT methods developed to study these

  2. Natural products mediating ecological interactions in Antarctic benthic communities: a mini-review of the known molecules.

    Science.gov (United States)

    Núñez-Pons, L; Avila, C

    2015-07-01

    Out of the many bioactive compounds described from the oceans, only a small fraction have been studied for their ecological significance. Similarly, most chemically mediated interactions are not well understood, because the molecules involved remain unrevealed. In Antarctica, this gap in knowledge is even more acute in comparison to tropical or temperate regions, even though polar organisms are also prolific producers of chemical defenses, and pharmacologically relevant products are being reported from the Southern Ocean. The extreme and unique marine environments surrounding Antarctica along with the numerous unusual interactions taking place in benthic communities are expected to select for novel functional secondary metabolites. There is an urgent need to comprehend the evolutionary role of marine derived substances in general, and particularly at the Poles, since molecules of keystone significance are vital in species survival, and therefore, in structuring the communities. Here we provide a mini-review on the identified marine natural products proven to have an ecological function in Antarctic ecosystems. This report recapitulates some of the bibliography from original Antarctic reviews, and updates the new literature in the field from 2009 to the present.

  3. When polarons meet polaritons: Exciton-vibration interactions in organic molecules strongly coupled to confined light fields

    Science.gov (United States)

    Wu, Ning; Feist, Johannes; Garcia-Vidal, Francisco J.

    2016-11-01

    We present a microscopic semianalytical theory for the description of organic molecules interacting strongly with a cavity mode. Exciton-vibration coupling within the molecule and exciton-cavity interaction are treated on an equal footing by employing a temperature-dependent variational approach. The interplay between strong exciton-vibration coupling and strong exciton-cavity coupling gives rise to a hybrid ground state, which we refer to as the lower polaron polariton. Explicit expressions for the ground-state wave function, the zero-temperature quasiparticle weight of the lower polaron polariton, the photoluminescence line strength, and the mean number of vibrational quanta are obtained in terms of the optimal variational parameters. The dependence of these quantities upon the exciton-cavity coupling strength reveals that strong cavity coupling leads to an enhanced vibrational dressing of the cavity mode, and at the same time a vibrational decoupling of the dark excitons, which in turn results in a lower polaron polariton resembling a single-mode dressed bare lower polariton in the strong-coupling regime. Thermal effects on several observables are briefly discussed.

  4. Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

    Directory of Open Access Journals (Sweden)

    Sergey V. Antipov

    2017-11-01

    Full Text Available Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

  5. Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

    Science.gov (United States)

    Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

    2017-11-01

    Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

  6. Rapid sampling of stochastic displacements in Brownian dynamics simulations with stresslet constraints

    Science.gov (United States)

    Fiore, Andrew M.; Swan, James W.

    2018-01-01

    Brownian Dynamics simulations are an important tool for modeling the dynamics of soft matter. However, accurate and rapid computations of the hydrodynamic interactions between suspended, microscopic components in a soft material are a significant computational challenge. Here, we present a new method for Brownian dynamics simulations of suspended colloidal scale particles such as colloids, polymers, surfactants, and proteins subject to a particular and important class of hydrodynamic constraints. The total computational cost of the algorithm is practically linear with the number of particles modeled and can be further optimized when the characteristic mass fractal dimension of the suspended particles is known. Specifically, we consider the so-called "stresslet" constraint for which suspended particles resist local deformation. This acts to produce a symmetric force dipole in the fluid and imparts rigidity to the particles. The presented method is an extension of the recently reported positively split formulation for Ewald summation of the Rotne-Prager-Yamakawa mobility tensor to higher order terms in the hydrodynamic scattering series accounting for force dipoles [A. M. Fiore et al., J. Chem. Phys. 146(12), 124116 (2017)]. The hydrodynamic mobility tensor, which is proportional to the covariance of particle Brownian displacements, is constructed as an Ewald sum in a novel way which guarantees that the real-space and wave-space contributions to the sum are independently symmetric and positive-definite for all possible particle configurations. This property of the Ewald sum is leveraged to rapidly sample the Brownian displacements from a superposition of statistically independent processes with the wave-space and real-space contributions as respective covariances. The cost of computing the Brownian displacements in this way is comparable to the cost of computing the deterministic displacements. The addition of a stresslet constraint to the over-damped particle

  7. Interactive measurement and characterization of DNA molecules by analysis of AFM images

    Czech Academy of Sciences Publication Activity Database

    Marek, J.; Demjénová, E.; Tomori, Z.; Janáček, Jiří; Zolotová, I.; Valle, F.; Favre, M.; Dietler, G.

    2005-01-01

    Roč. 63, č. 2 (2005), s. 87-93 ISSN 1552-4922 Grant - others:VEGA(SK) 5048; VEGA(SK) 2185; CZ-SK(CZ) KONTAKT 139; Swiss National Science Foundation(CH) 2100-063746.00/1 Institutional research plan: CEZ:AV0Z5011922 Keywords : DNA * atomic force microscopy * interactive image analysis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.115, year: 2005

  8. Interactions of molecules with surfaces. Progress report, 1 February 1985-31 January 1986

    International Nuclear Information System (INIS)

    Greene, E.F.

    1986-01-01

    The angular distributions of beams of Ne and Ar atoms scattered nearly elastically from LiF (100) at 294 K show structure that is obscured by inelastic scattering when the whole range of velocities leaving the crystal is recorded. Increased fluxes of neutral species in beams from an effusive source of alkali halide vapor observed when a beam of electrons is coaxial with the neutral beam are shown to be well accounted for by a model involving electron stimulated desorption of alkali atoms. A simple model is proposed for the compensation observed for changes of the preexponential factor and activation energy in rate coefficients for the desorption of molecules from surfaces undergoing surface phase transitions. The isomerization of perfluoroDewarbenzene to perfluorobenzene can be produced in yields of 10% after single energetic collisions with a surface of polytetrafluoroethylene. The yield of ions produced when a beam of Na atoms strikes a Si(111) surface is increased over the equilibrium value observed for thermal beams by a factor of 10 or more when the kinetic energy of the incoming atoms is increased to 14 eV. The yield is sensitive to the dynamics of electron exchange between the surface and the ion. 12 refs., 1 fig

  9. International Conference on the Interaction of atoms, molecules and plasmas with intense ultrashort laser pulses. Book of abstracts

    International Nuclear Information System (INIS)

    2006-01-01

    International Conference on the Interaction of atoms, molecules and plasmas with intense ultrashort laser pulses was held in Hungary in 2006. This conference which joined the ULTRA COST activity ('Laser-matter interactions with ultra-short pulses, high-frequency pulses and ultra-intense pulses. From attophysics to petawatt physics') and the XTRA ('Ultrashort XUV Pulses for Time-Resolved and Non-Linear Applications') Marie-Curie Research Training Network, intends to offer a possibility to the members of both of these activities to exchange ideas on recent theoretical and experimental results on the interaction of ultrashort laser pulses with matter giving a broad view from theoretical models to practical and technical applications. Ultrashort laser pulses reaching extra high intensities open new windows to obtain information about molecular and atomic processes. These pulses are even able to penetrate into atomic scalelengths not only by generating particles of ultrahigh energy but also inside the spatial and temporal atomic scalelengths. New regimes of laser-matter interaction were opened in the last decade with an increasing number of laboratories and researchers in these fields. (S.I.)

  10. Crossreactive T Cells Spotlight the Germline Rules for [alpha beta] T Cell-Receptor Interactions with MHC Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Shaodong; Huseby, Eric S.; Rubtsova, Kira; Scott-Browne, James; Crawford, Frances; Macdonald, Whitney A.; Marrack, Philippa; Kappler, John W. (HHMI); (NJMRC)

    2008-10-31

    To test whether highly crossreactive {alpha}{beta} T cell receptors (TCRs) produced during limited negative selection best illustrate evolutionarily conserved interactions between TCR and major histocompatibility complex (MHC) molecules, we solved the structures of three TCRs bound to the same MHC II peptide (IA{sup b}-3K). The TCRs had similar affinities for IA{sup b}-3K but varied from noncrossreactive to extremely crossreactive with other peptides and MHCs. Crossreactivity correlated with a shrinking, increasingly hydrophobic TCR-ligand interface, involving fewer TCR amino acids. A few CDR1 and CDR2 amino acids dominated the most crossreactive TCR interface with MHC, including V{beta}8 48Y and 54E and V{alpha}4 29Y, arranged to impose the familiar diagonal orientation of TCR on MHC. These interactions contribute to MHC binding by other TCRs using related V regions, but not usually so dominantly. These data show that crossreactive TCRs can spotlight the evolutionarily conserved features of TCR-MHC interactions and that these interactions impose the diagonal docking of TCRs on MHC.

  11. Adsorption geometry of tetracene on SiO 2/Si (1 1 1) substrate with the balance of molecule-substrate and intermolecular interaction

    Science.gov (United States)

    Mao, Hongying; Guan, Dandan; Chen, Meiliang; Dou, Weidong; Song, Fei; Zhang, Hanjie; Li, Haiyang; He, Pimo; Bao, Shining

    2010-02-01

    The growth of tetracene on SiO 2/Si(1 1 1) substrate has been studied by ultraviolet photoemission spectroscopy measurements. Seven emission features of the organic material are located at 2.26, 3.56, 4.77, 5.88, 6.98, 8.18 and 9.90 eV, respectively, below the Fermi level. The changes in binding energy and work function during the deposition of tetracene molecules on SiO 2 substrate indicate an interaction between tetracene molecule and substrate. The interaction between tetracene molecule and substrate is weaker than that between the organic and silicon substrate. The reduction in work function is due to the formation of interface dipole. Based on the density functional theory (DFT) calculation, tetracene molecules are arranged in an upright standing manner with the optimal growth of a small cluster consisting four molecules.

  12. Assessing Specific Oligonucleotides and Small Molecule Antibiotics for the Ability to Inhibit the CRD-BP-CD44 RNA Interaction

    Science.gov (United States)

    Thomsen, Dana; Lee, Chow H.

    2014-01-01

    Studies on Coding Region Determinant-Binding Protein (CRD-BP) and its orthologs have confirmed their functional role in mRNA stability and localization. CRD-BP is present in extremely low levels in normal adult tissues, but it is over-expressed in many types of aggressive human cancers and in neonatal tissues. Although the exact role of CRD-BP in tumour progression is unclear, cumulative evidence suggests that its ability to physically associate with target mRNAs is an important criterion for its oncogenic role. CRD-BP has high affinity for the 3′UTR of the oncogenic CD44 mRNA and depletion of CRD-BP in cells led to destabilization of CD44 mRNA, decreased CD44 expression, reduced adhesion and disruption of invadopodia formation. Here, we further characterize the CRD-BP-CD44 RNA interaction and assess specific antisense oligonucleotides and small molecule antibiotics for their ability to inhibit the CRD-BP-CD44 RNA interaction. CRD-BP has a high affinity for binding to CD44 RNA nts 2862–3055 with a Kd of 645 nM. Out of ten antisense oligonucleotides spanning nts 2862–3055, only three antisense oligonucleotides (DD4, DD7 and DD10) were effective in competing with CRD-BP for binding to 32P-labeled CD44 RNA. The potency of DD4, DD7 and DD10 in inhibiting the CRD-BP-CD44 RNA interaction in vitro correlated with their ability to specifically reduce the steady-state level of CD44 mRNA in cells. The aminoglycoside antibiotics neomycin, paramomycin, kanamycin and streptomycin effectively inhibited the CRD-BP-CD44 RNA interaction in vitro. Assessing the potential inhibitory effect of aminoglycoside antibiotics including neomycin on the CRD-BP-CD44 mRNA interaction in cells proved difficult, likely due to their propensity to non-specifically bind nucleic acids. Our results have important implications for future studies in finding small molecules and nucleic acid-based inhibitors that interfere with protein-RNA interactions. PMID:24622399

  13. Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair.

    Science.gov (United States)

    Liao, Yi; Schroeder, Jeremy W; Gao, Burke; Simmons, Lyle A; Biteen, Julie S

    2015-12-15

    MutS is responsible for initiating the correction of DNA replication errors. To understand how MutS searches for and identifies rare base-pair mismatches, we characterized the dynamic movement of MutS and the replisome in real time using superresolution microscopy and single-molecule tracking in living cells. We report that MutS dynamics are heterogeneous in cells, with one MutS population exploring the nucleoid rapidly, while another MutS population moves to and transiently dwells at the replisome region, even in the absence of appreciable mismatch formation. Analysis of MutS motion shows that the speed of MutS is correlated with its separation distance from the replisome and that MutS motion slows when it enters the replisome region. We also show that mismatch detection increases MutS speed, supporting the model for MutS sliding clamp formation after mismatch recognition. Using variants of MutS and the replication processivity clamp to impair mismatch repair, we find that MutS dynamically moves to and from the replisome before mismatch binding to scan for errors. Furthermore, a block to DNA synthesis shows that MutS is only capable of binding mismatches near the replisome. It is well-established that MutS engages in an ATPase cycle, which is necessary for signaling downstream events. We show that a variant of MutS with a nucleotide binding defect is no longer capable of dynamic movement to and from the replisome, showing that proper nucleotide binding is critical for MutS to localize to the replisome in vivo. Our results provide mechanistic insight into the trafficking and movement of MutS in live cells as it searches for mismatches.

  14. Analysis of vibronic interactions in the molecules of cross-conjugated ketones

    Directory of Open Access Journals (Sweden)

    Kompaneez V.V.

    2017-01-01

    Full Text Available We have done quantitative analysis of vibronic parameters of two cross-conjugated δ-dimethylaminoketones. The research shows the influence of С-N and C=O bonds in the rings, and the radicals with nitro compounds on the vibronic parameters of characteristic bands, which describe the state (vibrations, types of deformation under excitation of the phenyl ring and the polyene bridge. Results described impact of the substituent’s nature on the parameters of intra- and intermolecular interactions presents for the studied compounds.

  15. Label-free solution-based kinetic study of aptamer-small molecule interactions by kinetic capillary electrophoresis with UV detection revealing how kinetics control equilibrium.

    Science.gov (United States)

    Bao, Jiayin; Krylova, Svetlana M; Reinstein, Oren; Johnson, Philip E; Krylov, Sergey N

    2011-11-15

    Here we demonstrate a label-free solution-based approach for studying the kinetics of biopolymer-small molecule interactions. The approach utilizes kinetic capillary electrophoresis (KCE) separation and UV light absorption detection of the unlabeled small molecule. In this proof-of-concept work, we applied KCE-UV to study kinetics of interaction between a small molecule and a DNA aptamer. From the kinetic analysis of a series of aptamers, we found that dissociation rather than binding controls the stability of the complex. Because of its label-free features and generic nature, KCE-UV promises to become a practical tool for challenging kinetic studies of biopolymer-small molecule interactions.

  16. Brownian gas models for extreme-value laws

    International Nuclear Information System (INIS)

    Eliazar, Iddo

    2013-01-01

    In this paper we establish one-dimensional Brownian gas models for the extreme-value laws of Gumbel, Weibull, and Fréchet. A gas model is a countable collection of independent particles governed by common diffusion dynamics. The extreme-value laws are the universal probability distributions governing the affine scaling limits of the maxima and minima of ensembles of independent and identically distributed one-dimensional random variables. Using the recently introduced concept of stationary Poissonian intensities, we construct two gas models whose global statistical structures are stationary, and yield the extreme-value laws: a linear Brownian motion gas model for the Gumbel law, and a geometric Brownian motion gas model for the Weibull and Fréchet laws. The stochastic dynamics of these gas models are studied in detail, and closed-form analytical descriptions of their temporal correlation structures, their topological phase transitions, and their intrinsic first-passage-time fluxes are presented. (paper)

  17. Stochastic calculus for fractional Brownian motion and related processes

    CERN Document Server

    Mishura, Yuliya S

    2008-01-01

    The theory of fractional Brownian motion and other long-memory processes are addressed in this volume. Interesting topics for PhD students and specialists in probability theory, stochastic analysis and financial mathematics demonstrate the modern level of this field. Among these are results about Levy characterization of fractional Brownian motion, maximal moment inequalities for Wiener integrals including the values 0Brownian SDE. The author develops optimal filtering of mixed models including linear case, and studies financial applications and statistical inference with hypotheses testing and parameter estimation. She proves that the market with stock guided by the mixed model is arbitrage-free without any restriction on the dependence of the components and deduces different forms of the Black-Scholes equation for fractional mark...

  18. Deterministic Brownian motion generated from differential delay equations.

    Science.gov (United States)

    Lei, Jinzhi; Mackey, Michael C

    2011-10-01

    This paper addresses the question of how Brownian-like motion can arise from the solution of a deterministic differential delay equation. To study this we analytically study the bifurcation properties of an apparently simple differential delay equation and then numerically investigate the probabilistic properties of chaotic solutions of the same equation. Our results show that solutions of the deterministic equation with randomly selected initial conditions display a Gaussian-like density for long time, but the densities are supported on an interval of finite measure. Using these chaotic solutions as velocities, we are able to produce Brownian-like motions, which show statistical properties akin to those of a classical Brownian motion over both short and long time scales. Several conjectures are formulated for the probabilistic properties of the solution of the differential delay equation. Numerical studies suggest that these conjectures could be "universal" for similar types of "chaotic" dynamics, but we have been unable to prove this.

  19. Cosmophysical Factors in the Fluctuation Amplitude Spectrum of Brownian Motion

    Directory of Open Access Journals (Sweden)

    Kaminsky A. V.

    2010-04-01

    Full Text Available Phenomenon of the regular variability of the fine structure of the fluctuation in the amplitude distributions (shapes of related histograms for the case of Brownian motion was investigated. We took an advantage of the dynamic light scattering method (DLS to get a stochastically fluctuated signal determined by Brownian motion. Shape of the histograms is most likely to vary, synchronous, in two proximally located independent cells containing Brownian particles. The synchronism persists in the cells distant at 2m from each other, and positioned meridionally. With a parallel-wise positioning of the cells, high probability of the synchronous variation in the shape of the histograms by local time has been observed. This result meets the previous conclusion about the dependency of histogram shapes ("fluctuation amplitudes" of the spectra of stochastic processes upon rotation of the Earth.

  20. Cosmophysical Factors in the Fluctuation Amplitude Spectrum of Brownian Motion

    Directory of Open Access Journals (Sweden)

    Kaminsky A. V.

    2010-07-01

    Full Text Available Phenomenon of the regular variability of the fine structure of the fluctuation in the am- plitude distributions (shapes of related histograms for the case of Brownian motion was investigated. We took an advantage of the dynamic light scattering method (DLS to get a stochastically fluctuated signal determined by Brownian motion. Shape of the histograms is most likely to vary, synchronous, in two proximally located independent cells containing Brownian particles. The synchronism persists in the cells distant at 2 m from each other, and positioned meridionally. With a parallel-wise positioning of the cells, high probability of the synchronous variation in the shape of the histograms by local time has been observed. This result meets the previous conclusion about the dependency of histogram shapes (“fluctuation amplitudes” of the spectra of stochastic processes upon rotation of the Earth.

  1. Quantum Brownian motion model for the stock market

    Science.gov (United States)

    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.

  2. Non-colliding Brownian Motions and the Extended Tacnode Process

    Science.gov (United States)

    Johansson, Kurt

    2013-04-01

    We consider non-colliding Brownian motions with two starting points and two endpoints. The points are chosen so that the two groups of Brownian motions just touch each other, a situation that is referred to as a tacnode. The extended kernel for the determinantal point process at the tacnode point is computed using new methods and given in a different form from that obtained for a single time in previous work by Delvaux, Kuijlaars and Zhang. The form of the extended kernel is also different from that obtained for the extended tacnode kernel in another model by Adler, Ferrari and van Moerbeke. We also obtain the correlation kernel for a finite number of non-colliding Brownian motions starting at two points and ending at arbitrary points.

  3. Effective Potential Energies and Transport Cross Sections for Atom-Molecule Interactions of Nitrogen and Nitrogen

    Science.gov (United States)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene; Arnold, Jim (Technical Monitor)

    2001-01-01

    The potential energy surfaces for H2-N and N2-N interactions are calculated by accurate ab initio methods and applied to determine transport data. The results confirm that an effective potential energy for accurately determining transport properties can be calculated using a single orientation. A simple method is developed to determine the dispersion coefficients of effective potential energies Effective potential energies required for O2-O collisions are determ=ined. The H2-N, N2-N, O2-H, and O2-O collision integrals are calculated and tabulated for a large range of temperatures. The theoretical values of the N2-N and O2-O diffusion coefficients compare well with measured data available at room temperature.

  4. Exponential functionals of Brownian motion, I: Probability laws at fixed time

    OpenAIRE

    Matsumoto, Hiroyuki; Yor, Marc

    2005-01-01

    This paper is the first part of our survey on various results about the distribution of exponential type Brownian functionals defined as an integral over time of geometric Brownian motion. Several related topics are also mentioned.

  5. Probing the interactions of organic molecules, nanomaterials, and microbes with solid surfaces using quartz crystal microbalances: methodology, advantages, and limitations.

    Science.gov (United States)

    Huang, Rixiang; Yi, Peng; Tang, Yuanzhi

    2017-06-21

    Quartz crystal microbalances (QCMs) provide a new analytical opportunity and prospect to characterize many environmental processes at solid/liquid interfaces, thanks to their almost real-time measurement of physicochemical changes on their quartz sensor. This work reviews the applications of QCMs in probing the interactions of organic molecules, nanomaterials (NMs) and microbes with solid surfaces. These interfacial interactions are relevant to critical environmental processes such as biofilm formation, fate and transport of NMs, fouling in engineering systems and antifouling practices. The high sensitivity, real-time monitoring, and simultaneous frequency and dissipation measurements make QCM-D a unique technique that helps reveal the interaction mechanisms for the abovementioned processes (e.g., driving forces, affinity, kinetics, and the interplay between surface chemistry and solution chemistry). On the other hand, QCM measurement is nonselective and spatially-dependent. Thus, caution should be taken during data analysis and interpretation, and it is necessary to cross-validate the results using complementary information from other techniques for more quantitative and accurate interpretation. This review summarizes the general methodologies for collecting and analyzing raw QCM data, as well as for evaluating the associated uncertainties. It serves to help researchers gain deeper insights into the fundamentals and applications of QCMs, and provides new perspectives on future research directions.

  6. The Intersection Probability of Brownian Motion and SLEκ

    Directory of Open Access Journals (Sweden)

    Shizhong Zhou

    2015-01-01

    Full Text Available By using excursion measure Poisson kernel method, we obtain a second-order differential equation of the intersection probability of Brownian motion and SLEκ. Moreover, we find a transformation such that the second-order differential equation transforms into a hypergeometric differential equation. Then, by solving the hypergeometric differential equation, we obtain the explicit formula of the intersection probability for the trace of the chordal SLEκ and planar Brownian motion started from distinct points in an upper half-plane H-.

  7. Stochastic flows in the Brownian web and net

    Czech Academy of Sciences Publication Activity Database

    Schertzer, E.; Sun, R.; Swart, Jan M.

    2014-01-01

    Roč. 227, č. 1065 (2014), s. 1-160 ISSN 0065-9266 R&D Projects: GA ČR GA201/07/0237; GA ČR GA201/09/1931 Institutional support: RVO:67985556 Keywords : Brownian web * Brownian net * stochastic flow of kernels * measure-valued process * Howitt-Warren flow * linear system * random walk in random environment * finite graph representation Subject RIV: BA - General Mathematics Impact factor: 1.727, year: 2014 http://library.utia.cas.cz/separaty/2013/SI/swart-0396636.pdf

  8. Generalized Multifractional Brownian Motion: Definition and Preliminary Results

    OpenAIRE

    Ayache, Antoine; Lévy Véhel, Jacques

    1999-01-01

    The Multifractional Brownian Motion (MBM) is a generalization of the well known Fractional Brownian Motion. One of the main reasons that makes the MBM interesting for modelization, is that one can prescribe its regularity: given any Hölder function H(t), with values in ]0,1[, one can construct an MBM admitting at any t0, a Hölder exponent equal to H(t0). However, the continuity of the function H(t) is sometimes undesirable, since it restricts the field of application. In this work we define a...

  9. Brownian motion with adhesion: harmonic oscillator with fluctuating mass.

    Science.gov (United States)

    Gitterman, M; Klyatskin, V I

    2010-05-01

    In contrast to the cases usually studied of a harmonic oscillator subject to a random force (Brownian motion) or having random frequency or random damping, we consider a random mass which corresponds to an oscillator for which the particles of the surrounding medium adhere to it for some (random) time after the collision, thereby changing the oscillator mass. This model, which describes Brownian motion with adhesion, can be useful for the analysis of chemical and biological solutions as well as nanotechnological devices. We consider dichotomous noise and its limiting case, white noise.

  10. Single potassium niobate nano/microsized particles as local mechano-optical Brownian probes

    Science.gov (United States)

    Mor, Flavio M.; Sienkiewicz, Andrzej; Magrez, Arnaud; Forró, László; Jeney, Sylvia

    2016-03-01

    Perovskite alkaline niobates, due to their strong nonlinear optical properties, including birefringence and the capability to produce second-harmonic generation (SHG) signals, attract a lot of attention as potential candidates for applications as local nano/microsized mechano-optical probes. Here, we report on an implementation of photonic force microscopy (PFM) to explore the Brownian motion and optical trappability of monocrystalline potassium niobate (KNbO3) nano/microsized particles having sizes within the range of 50 to 750 nm. In particular, we exploit the anisotropic translational diffusive regime of the Brownian motion to quantify thermal fluctuations and optical forces of singly-trapped KNbO3 particles within the optical trapping volume of a PFM microscope. We also show that, under near-infrared (NIR) excitation of the highly focused laser beam of the PFM microscope, a single optically-trapped KNbO3 particle reveals a strong SHG signal manifested by a narrow peak (λem = 532 nm) at half the excitation wavelength (λex = 1064 nm). Moreover, we demonstrate that the thus induced SHG emission can be used as a local light source that is capable of optically exciting molecules of an organic dye, Rose Bengal (RB), which adhere to the particle surface, through the mechanism of luminescence energy transfer (LET).Perovskite alkaline niobates, due to their strong nonlinear optical properties, including birefringence and the capability to produce second-harmonic generation (SHG) signals, attract a lot of attention as potential candidates for applications as local nano/microsized mechano-optical probes. Here, we report on an implementation of photonic force microscopy (PFM) to explore the Brownian motion and optical trappability of monocrystalline potassium niobate (KNbO3) nano/microsized particles having sizes within the range of 50 to 750 nm. In particular, we exploit the anisotropic translational diffusive regime of the Brownian motion to quantify thermal

  11. Theoretical estimation of optical hyperpolarizability appearance in fullerene molecule and carbon nanotubes interacting with ionic crystal surface

    Science.gov (United States)

    Mestechkin, M. M.

    2007-05-01

    The first hyperpolarizability (HP) of fullerene and finite length carbon nanotubes (FCN), attached to the neutral surfaces of SiO 2 (1 1 0), CdS(1 1 2 0), and CdTe(1 1 0) crystals, is calculated in the framework of the semi-empirical version of the time-dependent Hartree-Fock theory (TDHF). The norm of β-vector invariant, induced by the substrate, is of the same order as in some organic molecules with the observed nonlinear optical properties. The orthogonal to the substrate β-component is responsible for generation of the second harmonic by fullerene according to Hoshi and co-authors [H. Hoshi, N. Nakamura, Y. Maruyama, T. Nakagawa, S. Suzuki, H. Shiromaru, Y. Achiba, Jpn. J. Appl. Phys. 30 (1991) L1397]. The calculated value of this component is shown sufficient for the weak generation. It is found that zig-zag FCN, in contrast to armchair FCN, are characterized by the resonant behaviour of HP for second harmonic generation (SHG) at low frequencies due to the existence of quasi-degenerate (hyperbolic) levels in the close vicinity of the Fermi level. This ability is created by the external ionic crystal potential and affected by mutual electron interaction of molecules in the layer.

  12. Divacancy-assisted transition metal adsorption on the BN graphene and its interaction with hydrogen molecules: a theoretical study

    Science.gov (United States)

    Chen, Ying; Wang, Hongmei; Wang, Hongxia; Zhao, Jing-xiang; Cai, Qing-hai; Wang, Xiao-Guang; Ding, Yi-hong

    2013-05-01

    We have performed first-principles calculations to study the chemical functionalization of the BN graphene with divacancy (DV) defect by 12 different transition metal (TM) atoms, including Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pt, and Au. The results indicate that the DV defect can assist the adsorption of TM atoms on BN graphene. Moreover, some impurity bands are induced within the band gap of DV-BN graphene, leading to the modification of its electronic properties in various ways. Interestingly, Ti- and Co-adsorbed DV-BN graphenes are found to possess ferromagnetic characteristic, while antiferromagnetic state is preferred for V-, Mn-, and Fe-functionalized DV-BN graphenes, and the paramagnetic state is the ground state for Sc-, Cr-, Ni-, Cu, Zn-, Pt-, and Au-decorated DV-BN graphenes. Finally, aiming at evaluating the potential of these functionalized BN graphenes in hydrogen storage, we study their interaction with H2 molecules. It is found that the dispersed Sc, V, and Cr on DV-BN graphene are able to adsorb up to three H2 molecules as strongly as 0.25-0.58 eV/H2, suggesting that the three nanomaterials may be suitable candidates for hydrogen storage.

  13. Divacancy-assisted transition metal adsorption on the BN graphene and its interaction with hydrogen molecules: a theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Ying; Wang, Hongmei; Wang, Hongxia [Key Laboratory for Photoelectric Bandgap Materials, Ministry of Education, Harbin Normal University, Harbin 150025 (China); Zhao, Jing-xiang, E-mail: xjz_hmily@yahoo.com.cn [Key Laboratory for Photoelectric Bandgap Materials, Ministry of Education, Harbin Normal University, Harbin 150025 (China); Cai, Qing-hai; Wang, Xiao-Guang [Key Laboratory for Photoelectric Bandgap Materials, Ministry of Education, Harbin Normal University, Harbin 150025 (China); Ding, Yi-hong, E-mail: yhdd@jlu.edu.cn [State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023 (China)

    2013-05-15

    We have performed first-principles calculations to study the chemical functionalization of the BN graphene with divacancy (DV) defect by 12 different transition metal (TM) atoms, including Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pt, and Au. The results indicate that the DV defect can assist the adsorption of TM atoms on BN graphene. Moreover, some impurity bands are induced within the band gap of DV-BN graphene, leading to the modification of its electronic properties in various ways. Interestingly, Ti- and Co-adsorbed DV-BN graphenes are found to possess ferromagnetic characteristic, while antiferromagnetic state is preferred for V-, Mn-, and Fe-functionalized DV-BN graphenes, and the paramagnetic state is the ground state for Sc-, Cr-, Ni-, Cu, Zn-, Pt-, and Au-decorated DV-BN graphenes. Finally, aiming at evaluating the potential of these functionalized BN graphenes in hydrogen storage, we study their interaction with H{sub 2} molecules. It is found that the dispersed Sc, V, and Cr on DV-BN graphene are able to adsorb up to three H{sub 2} molecules as strongly as 0.25–0.58 eV/H{sub 2}, suggesting that the three nanomaterials may be suitable candidates for hydrogen storage.

  14. CHIPMUNK: A Virtual Synthesizable Small-Molecule Library for Medicinal Chemistry, Exploitable for Protein-Protein Interaction Modulators.

    Science.gov (United States)

    Humbeck, Lina; Weigang, Sebastian; Schäfer, Till; Mutzel, Petra; Koch, Oliver

    2018-03-20

    A common issue during drug design and development is the discovery of novel scaffolds for protein targets. On the one hand the chemical space of purchasable compounds is rather limited; on the other hand artificially generated molecules suffer from a grave lack of accessibility in practice. Therefore, we generated a novel virtual library of small molecules which are synthesizable from purchasable educts, called CHIPMUNK (CHemically feasible In silico Public Molecular UNiverse Knowledge base). Altogether, CHIPMUNK covers over 95 million compounds and encompasses regions of the chemical space that are not covered by existing databases. The coverage of CHIPMUNK exceeds the chemical space spanned by the Lipinski rule of five to foster the exploration of novel and difficult target classes. The analysis of the generated property space reveals that CHIPMUNK is well suited for the design of protein-protein interaction inhibitors (PPIIs). Furthermore, a recently developed structural clustering algorithm (StruClus) for big data was used to partition the sub-libraries into meaningful subsets and assist scientists to process the large amount of data. These clustered subsets also contain the target space based on ChEMBL data which was included during clustering. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Controlling the formation process and atomic structures of single pyrazine molecular junction by tuning the strength of the metal-molecule interaction.

    Science.gov (United States)

    Kaneko, Satoshi; Takahashi, Ryoji; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

    2017-04-12

    The formation process and atomic structures were investigated for single pyrazine molecular junctions sandwiched by three different Au, Ag, and Cu electrodes using a mechanically controllable break junction technique in ultrahigh vacuum conditions at 300 K. We demonstrated that the formation process of the single-molecule junction crucially depended on the choice of the metal electrodes. While single-molecule junction showing two distinct conductance states were found for the Au electrodes, only the single conductance state was evident for the Ag electrodes, and there was no junction formation for the Cu electrodes. These results suggested that metal-molecule interaction dominates the formation process and probability of the single-molecule junction. In addition to the metal-molecule interaction, temperature affected the formation process of the single-molecule junction. The single pyrazine molecular junction formed between Au electrodes exhibited significant temperature dependence where the junction-formation probability was about 8% at 300 K, while there was no junction-formation at 100 K. Instead of the junction formation, an Au atomic wire was formed at the low temperature. This study provides insight into the tuning of the junction-forming process for single-molecule junctions, which is needed to construct device structures on a single molecule scale.

  16. Fibronectin type III (FN3) modules of the neuronal cell adhesion molecule L1 interact directly with the fibroblast growth factor (FGF) receptor

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Li, Shizhong; Hinsby, Anders Mørkeberg

    2008-01-01

    The neuronal cell adhesion molecule (CAM) L1 promotes axonal outgrowth, presumably through an interaction with the fibroblast growth factor receptor (FGFR). The present study demonstrates a direct interaction between L1 fibronectin type III (FN3) modules I-V and FGFR1 immunoglobulin (Ig) modules II...

  17. The Composition-Tunable Polydiacetylenic Complex Films: Conformational Change upon Thermal Stimulation and Preferential Interaction with Specific Small Molecules

    Directory of Open Access Journals (Sweden)

    Chao Wang

    2017-01-01

    Full Text Available Polydiacetylenic complex films were prepared using 10,12-pentacosadiynoic acid (PCDA and para-xylenediamine (pXDA upon acid-base interactions. The thermochromatic reversibility of the complex films was modulated by changing the mixed molar ratio (3 : 1, 2 : 1, and 1 : 1 of the two molecules. The corresponding conformational changes of the complex films were studied by ex situ FTIR analysis upon thermal stimulation for the first time. In addition, the binding specificities of α-, β-, and γ-cyclodextrins (CDs with the films were studied, where the α-CDs can induce stronger red fluorescent emission of the films. These fundamental results may be useful for platforms that use these polydiacetylenic complex films as optoelectronic devices or chemical/biological sensors.

  18. Interaction of hnRNP A1 with telomere DNA G-quadruplex structures studied at the single molecule level

    DEFF Research Database (Denmark)

    Krüger, Asger Christian; Raarup, Merete Krog; Nielsen, Morten Muhlig

    2010-01-01

    G-rich telomeric DNA sequences can form G-quadruplex structures. The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and a shortened derivative (UP1) are active in telomere length regulation, and it has been reported that UP1 can unwind G-quadruplex structures. Here, we investigate...... the interaction of hnRNP A1 with G-quadruplex DNA structures containing the human telomere repeat (TTAGGG) by gel retardation assays, ensemble fluorescence energy transfer (FRET) spectroscopy, and single molecule FRET microscopy. Our biochemical experiments show that hnRNP A1 binds well to the G...... to the previously reported crystal structures of UP1-telomere DNA complexes where the DNA oligo within the protein-DNA complex is in a fully open conformation....

  19. Plasma Interaction with Organic Molecules in Liquid as Fundamental Processes in Plasma Medicine.

    Science.gov (United States)

    Takenaka, Kosuke; Miyazaki, Atsushi; Abe, Hiroya; Uchida, Giichiro; Setsuhara, Yuichi

    2015-03-01

    Investigation of plasma-organic materials interaction in aqueous solution with atmospheric pressure plasmas have been carried out. Degradation of methylene blue (MB) in aqueous solution via atmospheric pressure He plasma exposure through gas/liquid interface have been investigated. The optical emission spectrum shows considerable emissions of He lines and the emission of O, OH and N radicals attributed to dissociation of water (H2O) and air has been confirmed. Structure variation of MB in solution treated with the atmospheric-pressure He plasma has been measured by Fourier transform infrared spectroscopy (FT-IR). The results obtained from FT-IR analysis show degradation of MB in solution treated with the atmospheric-pressure He plasma. The pH effect of MB degradation was investigated using controlled pH solutions by an ultraviolet-visible (UV-Vis) spectroscopy and FT-IR. The results show no effect of MB degradation on pH. The results exhibit that the atmospheric pressure plasmas exposure has made it possible to degrade organic materials in solution due to irradiated radicals from plasma through plasma/liquid interface.

  20. Interaction of ions, atoms, and small molecules with quantized vortex lines in superfluid (4)He.

    Science.gov (United States)

    Mateo, David; Eloranta, Jussi; Williams, Gary A

    2015-02-14

    The interaction of a number of impurities (H2, Ag, Cu, Ag2, Cu2, Li, He3 (+), He(*) ((3)S), He2 (∗) ((3)Σu), and e(-)) with quantized rectilinear vortex lines in superfluid (4)He is calculated by using the Orsay-Trento density functional theory (DFT) method at 0 K. The Donnelly-Parks (DP) potential function binding ions to the vortex is combined with DFT data, yielding the impurity radius as well as the vortex line core parameter. The vortex core parameter at 0 K (0.74 Å) obtained either directly from the vortex line geometry or through the DP potential fitting is smaller than previously suggested but is compatible with the value obtained from re-analysis of the Rayfield-Reif experiment. All of the impurities have significantly higher binding energies to vortex lines below 1 K than the available thermal energy, where the thermally assisted escape process becomes exponentially negligible. Even at higher temperatures 1.5-2.0 K, the trapping times for larger metal clusters are sufficiently long that the previously observed metal nanowire assembly in superfluid helium can take place at vortex lines. The binding energy of the electron bubble is predicted to decrease as a function of both temperature and pressure, which allows adjusting the trap depth for either permanent trapping or to allow thermally assisted escape. Finally, a new scheme for determining the trapping of impurities on vortex lines by optical absorption spectroscopy is outlined and demonstrated for He(*).

  1. A quartz crystal microbalance characterization of metal-oil interfaces and interactions with wax molecules

    Energy Technology Data Exchange (ETDEWEB)

    Paso, K.; Kompalla, T.; Braathen, B.; Sjoblom, J. [Norwegian Univ. of Science and Technology, Trondheim (Norway). Dept. of Chemical Engineering, Ugelstad Laboratory; Aske, N.; Ronningsen, H.P. [StatoilHydro, Stavanger (Norway); Viitala, T. [KSV Instruments, Helsinki (Finland)

    2008-07-01

    This study investigated the solid-liquid interface between stainless steel and model petroleum fluids at isothermal conditions using a quartz crystal microbalance. AISI 316 (Fe/Cr18/Ni10/Mo3) stainless steel was chosen to represent the metal surface, while paraffin components dissolved in dodecane constituted the petroleum model fluid. Commercial macro-crystalline and micro-crystalline waxes provided linear and branched paraffin components, respectively. A van't Hoff relationship was used to establish the paraffin solubility conditions. The well-defined solubility conditions were provided by model fluids prepared with the single-component alkanes n-C36 or n-C30 paraffin. According to the monitored changes in resonance frequency and dissipation factor of the quartz crystal resonator immersed in the model fluids, there was no continual deposition of paraffin components at isothermal conditions. Moreover, solid paraffin crystals dispersed in solution did not adhere to the stainless steel surface. The absence of attractive interactions between the stainless steel surface and dispersed paraffin crystals suggests that an axial transport mechanism exists for incipient wax deposit formation, where gelation kinetics play a key role. These conclusions were supported by QCM measurements performed under a thermal gradient.

  2. Differential interaction kinetics of a bipolar structure-specific endonuclease with DNA flaps revealed by single-molecule imaging.

    Directory of Open Access Journals (Sweden)

    Rachid Rezgui

    Full Text Available As DNA repair enzymes are essential for preserving genome integrity, understanding their substrate interaction dynamics and the regulation of their catalytic mechanisms is crucial. Using single-molecule imaging, we investigated the association and dissociation kinetics of the bipolar endonuclease NucS from Pyrococcus abyssi (Pab on 5' and 3'-flap structures under various experimental conditions. We show that association of the PabNucS with ssDNA flaps is largely controlled by diffusion in the NucS-DNA energy landscape and does not require a free 5' or 3' extremity. On the other hand, NucS dissociation is independent of the flap length and thus independent of sliding on the single-stranded portion of the flapped DNA substrates. Our kinetic measurements have revealed previously unnoticed asymmetry in dissociation kinetics from these substrates that is markedly modulated by the replication clamp PCNA. We propose that the replication clamp PCNA enhances the cleavage specificity of NucS proteins by accelerating NucS loading at the ssDNA/dsDNA junctions and by minimizing the nuclease interaction time with its DNA substrate. Our data are also consistent with marked reorganization of ssDNA and nuclease domains occurring during NucS catalysis, and indicate that NucS binds its substrate directly at the ssDNA-dsDNA junction and then threads the ssDNA extremity into the catalytic site. The powerful techniques used here for probing the dynamics of DNA-enzyme binding at the single-molecule have provided new insight regarding substrate specificity of NucS nucleases.

  3. Stability theorems for stochastic differential equations driven by G-Brownian motion

    OpenAIRE

    Zhang, Defei

    2011-01-01

    In this paper, stability theorems for stochastic differential equations and backward stochastic differential equations driven by G-Brownian motion are obtained. We show the existence and uniqueness of solutions to forward-backward stochastic differential equations driven by G-Brownian motion. Stability theorem for forward-backward stochastic differential equations driven by G-Brownian motion is also presented.

  4. Theoretical Study on Effects of Hydrogen-Bonding and Molecule-Cation Interactions on the Sensitivity of HMX.

    Science.gov (United States)

    Li, Yunlu; Wu, Junpeng; Cao, Duanlin; Wang, Jianlong

    2016-10-04

    To assess the effects of weak interactions on the sensitivity of HMX, eleven complexes of HMX (where six of them are hydrogen-bonding complexes, and the other five are molecular-cation complexes) have been studied via quantum chemical treatment. The geometric and electronic structures were determined using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df, 2p) and aug-cc-pVTZ basis sets. The changes of the bond dissociation energy (BDE) of the trigger bond (N-NO2 in HMX) and nitro group charge have been computed on the detail consideration to access the sensitivity changes of HMX. The results indicate that upon complex forming, the BDE increases and the charge of nitro group turns more negative in complexes, suggesting that the strength of the N-NO2 trigger bond is enhanced then the sensitivity of HMX is reduced. Atom-in-molecules analysis have also been carried to understand the nature of intermolecular interactions and the strength of trigger bonds.

  5. Thermodynamic laws and equipartition theorem in relativistic Brownian motion.

    Science.gov (United States)

    Koide, T; Kodama, T

    2011-06-01

    We extend the stochastic energetics to a relativistic system. The thermodynamic laws and equipartition theorem are discussed for a relativistic Brownian particle and the first and the second law of thermodynamics in this formalism are derived. The relation between the relativistic equipartition relation and the rate of heat transfer is discussed in the relativistic case together with the nature of the noise term.

  6. Brownian motion as a new probe of wettability

    Science.gov (United States)

    Mo, Jianyong; Simha, Akarsh; Raizen, Mark G.

    2017-04-01

    Understanding wettability is crucial for optimizing oil recovery, semiconductor manufacturing, pharmaceutical industry, and electrowetting. In this letter, we study the effects of wettability on Brownian motion. We consider the cases of a sphere in an unbounded fluid medium, as well as a sphere placed in the vicinity of a plane wall. For the first case, we show the effects of wettability on the statistical properties of the particles' motion, such as velocity autocorrelation, velocity, and thermal force power spectra over a large range of time scales. We also propose a new method to measure wettability based on the particles' Brownian motion. In addition, we compare the boundary effects on Brownian motion imposed by both no-slip and perfect-slip flat walls. We emphasize the surprising boundary effects on Brownian motion imposed by a perfect-slip wall in the parallel direction, such as a higher particle mobility parallel to a perfect flat wall compared to that in the absence of the wall, as well as compared to a particle near a no-slip flat wall.

  7. 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 ...

  8. Brownian Motion as a Limit to Physical Measuring Processes

    DEFF Research Database (Denmark)

    Niss, Martin

    2016-01-01

    formulated a general conclusion concerning the nature of physical measurements, namely that there is a definite limit to the ultimate sensitivity of measuring instruments beyond which we cannot advance, and that this limit is determined by Brownian motion. Ising’s conclusion agreed with experiments......, physicists in particular saw the work as an indication that noise is of practical relevance for their enterprise...

  9. 100 years of Einstein's Theory of Brownian Motion: From Pollen ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 11. 100 years of Einstein's Theory of Brownian Motion: From Pollen Grains to Protein Trains – 2. Debashish Chowdhury. General Article Volume 10 Issue 11 November 2005 pp 42-54 ...

  10. 100 years of Einstein's Theory of Brownian Motion: From Pollen ...

    Indian Academy of Sciences (India)

    ian motion was made by Gerlach [1] using a tiny mirror fixed on a very fine ... deterministic equation that describes the time evolution. Interestingly, three quarters of a century later the problem of rotational Brownian motion of a mirror was reinvestigated ... (geomagnetism), as the history of the earth's magnetic field remains ...

  11. Entropy production of a Brownian ellipsoid in the overdamped limit.

    Science.gov (United States)

    Marino, Raffaele; Eichhorn, Ralf; Aurell, Erik

    2016-01-01

    We analyze the translational and rotational motion of an ellipsoidal Brownian particle from the viewpoint of stochastic thermodynamics. The particle's Brownian motion is driven by external forces and torques and takes place in an heterogeneous thermal environment where friction coefficients and (local) temperature depend on space and time. Our analysis of the particle's stochastic thermodynamics is based on the entropy production associated with single particle trajectories. It is motivated by the recent discovery that the overdamped limit of vanishing inertia effects (as compared to viscous fricion) produces a so-called "anomalous" contribution to the entropy production, which has no counterpart in the overdamped approximation, when inertia effects are simply discarded. Here we show that rotational Brownian motion in the overdamped limit generates an additional contribution to the "anomalous" entropy. We calculate its specific form by performing a systematic singular perturbation analysis for the generating function of the entropy production. As a side result, we also obtain the (well-known) equations of motion in the overdamped limit. We furthermore investigate the effects of particle shape and give explicit expressions of the "anomalous entropy" for prolate and oblate spheroids and for near-spherical Brownian particles.

  12. Trajectories of Brownian particles with space-correlated noise

    Indian Academy of Sciences (India)

    The Langevin equation used to model Brownian motion includes a stochastic process that is routinely assumed to be a Gaussian white noise. Spatial correlations of the noise are usually ruled out, and the paths traced by the random walkers are statistically independent. In this study, I consider instead noise which is white in ...

  13. Suspended particle transport through constriction channel with Brownian motion

    DEFF Research Database (Denmark)

    Hanasaki, Itsuo; Walther, Jens Honore

    2017-01-01

    It is well known that translocation events of a polymer or rod through pores or narrower parts of micro- and nanochannels have a stochastic nature due to the Brownian motion. However, it is not clear whether the objects of interest need to have a larger size than the entrance to exhibit the devia...

  14. Markov-modulated Brownian motion with two reflecting barriers

    NARCIS (Netherlands)

    Ivanovs, J.

    2010-01-01

    We consider a Markov-modulated Brownian motion reflected to stay in a strip [0, B]. The stationary distribution of this process is known to have a simple form under some assumptions. We provide a short probabilistic argument leading to this result and explain its simplicity. Moreover, this argument

  15. Momentum conserving Brownian dynamics propagator for complex soft matter fluids

    NARCIS (Netherlands)

    Padding, J.T.; Briels, Willem J.

    2014-01-01

    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

  16. Microrheology of colloidal dispersions by Brownian dynamics simulations

    NARCIS (Netherlands)

    Carpen, I.C.; Brady, John F.; Brady, J.F.

    2005-01-01

    We investigate active particle-tracking microrheology in a colloidal dispersion by Brownian dynamics simulations. A probe particle is dragged through the dispersion with an externally imposed force in order to access the nonlinear viscoelastic response of the medium. The probe’s motion is governed

  17. High-Affinity, Small-Molecule Peptidomimetic Inhibitors of MLL1/WDR5 Protein-Protein Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Karatas, Hacer; Townsend, Elizabeth C; Cao, Fang; Chen, Yong; Bernard, Denzil; Liu, Liu; Lei, Ming; Dou, Yali; Wang, Shaomeng [Michigan; (HHMI)

    2013-02-12

    Mixed lineage leukemia 1 (MLL1) is a histone H3 lysine 4 (H3K4) methyltransferase, and targeting the MLL1 enzymatic activity has been proposed as a novel therapeutic strategy for the treatment of acute leukemia harboring MLL1 fusion proteins. The MLL1/WDR5 protein–protein interaction is essential for MLL1 enzymatic activity. In the present study, we designed a large number of peptidomimetics to target the MLL1/WDR5 interaction based upon -CO-ARA-NH–, the minimum binding motif derived from MLL1. Our study led to the design of high-affinity peptidomimetics, which bind to WDR5 with Ki < 1 nM and function as potent antagonists of MLL1 activity in a fully reconstituted in vitro H3K4 methyltransferase assay. Determination of co-crystal structures of two potent peptidomimetics in complex with WDR5 establishes their structural basis for high-affinity binding to WDR5. Evaluation of one such peptidomimetic, MM-102, in bone marrow cells transduced with MLL1-AF9 fusion construct shows that the compound effectively decreases the expression of HoxA9 and Meis-1, two critical MLL1 target genes in MLL1 fusion protein mediated leukemogenesis. MM-102 also specifically inhibits cell growth and induces apoptosis in leukemia cells harboring MLL1 fusion proteins. Our study provides the first proof-of-concept for the design of small-molecule inhibitors of the WDR5/MLL1 protein–protein interaction as a novel therapeutic approach for acute leukemia harboring MLL1 fusion proteins.

  18. Brownian dynamics of self-regulated particles with additional degrees of freedom: Symmetry breaking and homochirality

    Science.gov (United States)

    Bhattacharyya, Debankur; Paul, Shibashis; Ghosh, Shyamolina; Ray, Deb Shankar

    2018-04-01

    We consider the Brownian motion of a collection of particles each with an additional degree of freedom. The degree of freedom of a particle (or, in general, a molecule) can assume distinct values corresponding to certain states or conformations. The time evolution of the additional degree of freedom of a particle is guided by those of its neighbors as well as the temperature of the system. We show that the local averaging over these degrees of freedom results in emergence of a collective order in the dynamics in the form of selection or dominance of one of the isomers leading to a symmetry-broken state. Our statistical model captures the basic features of homochirality, e.g., autocatalysis and chiral inhibition.

  19. Functional interactions between voltage-gated Ca(2+) channels and Rab3-interacting molecules (RIMs): new insights into stimulus-secretion coupling.

    Science.gov (United States)

    Gandini, María A; Felix, Ricardo

    2012-03-01

    Stimulus-secretion coupling is a complex set of intracellular reactions initiated by an external stimulus that result in the release of hormones and neurotransmitters. Under physiological conditions this signaling process takes a few milliseconds, and to minimize delays cells have developed a formidable integrated network, in which the relevant molecules are tightly packed on the nanometer scale. Active zones, the sites of release, are composed of several different proteins including voltage-gated Ca(2+) (Ca(V)) channels. It is well acknowledged that hormone and neurotransmitter release is initiated by the activation of these channels located close to docked vesicles, though the mechanisms that enrich channels at release sites are largely unknown. Interestingly, Rab3 binding proteins (RIMs), a diverse multidomain family of proteins that operate as effectors of the small G protein Rab3 involved in secretory vesicle trafficking, have recently identified as binding partners of Ca(V) channels, placing both proteins in the center of an interaction network in the molecular anatomy of the active zones that influence different aspects of secretion. Here, we review recent evidences providing support for the notion that RIMs directly bind to the pore-forming and auxiliary β subunits of Ca(V) channels and with RIM-binding protein, another interactor of the channels. Through these interactions, RIMs regulate the biophysical properties of the channels and their anchoring relative to active zones, significantly influencing hormone and neurotransmitter release. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Vibronic Coupling and Electron-Phonon Interactions in Molecules and Crystals: XXIII International Symposium on the Jahn-Teller Effect

    International Nuclear Information System (INIS)

    2017-01-01

    ForewordThis issue of J. Phys. Conf. Series contains the proceedings of the 23"r"d International Symposium on the Jahn-Teller Effect with the main title “Vibronic coupling and electron-phonon interaction in molecules and crystals”, which took place in Tartu (Estonia), August 27-September 1, 2016, bringing together over 70 participants from various fields of physics and chemistry. More information on the symposium program can be found at https://ttl.ut.ee/jt16/.The series of mostly biannual Jahn-Teller symposia started in 1976. It addresses topics involving the coupling between electronic and nuclear motions in molecules and solids in conditions of electronic degeneracy and pseudodegeneracy. The Jahn-Teller effect, pseudo Jahn-Teller effect, and related vibronic coupling and electron-phonon interactions are responsible for structural instabilities and non-trivial dynamics in polyatomic systems, including pseudo-rotations and non-adiabatic effects around conical intersections and seams, and play a key role in the explanation of seemingly diverse phenomena, such as spontaneous symmetry breakings, structural phase transitions, colossal magnetoresistance, exotic molecular magnetism, superconductivity in fullerides, giant permittivity and flexoelectricity, and chemical reactions after thermo- or photoexcitation. The meeting brings together theoreticians and experimentalists working in molecular physics and chemistry with researches working in solid state physics.A characteristic of these symposia is that they are devoted to discussion of a wide range of physical and chemical phenomena which, at first sight, are different in scope and nature, but in fact they are strongly entangled by vibronic coupling, and their joint presentation and discussion is deemed to mutually enrich the presenters from different fields with stimulating novel ideas.The 23"r"d Symposium included the following topics:• Fundamental theory, computation, and experimental observation of vibronic

  1. Cell adhesion molecules in the development of inflammatory infiltrates in giant cell arteritis: inflammation-induced angiogenesis as the preferential site of leukocyte-endothelial cell interactions.

    Science.gov (United States)

    Cid, M C; Cebrián, M; Font, C; Coll-Vinent, B; Hernández-Rodríguez, J; Esparza, J; Urbano-Márquez, A; Grau, J M

    2000-01-01

    To investigate the expression pattern of adhesion molecules involved in leukocyte-endothelial cell interactions in giant cell arteritis (GCA). Immunohistochemical analysis was performed on frozen temporal artery sections from 32 patients with biopsy-proven GCA and from 12 control patients with other diseases. Adhesion molecules identified were intercellular adhesion molecule 1 (ICAM-1), ICAM-2, ICAM-3, vascular cell adhesion molecule 1 (VCAM-1), platelet endothelial cell adhesion molecule 1 (PECAM-1), E-selectin, P-selectin, L-selectin, lymphocyte function-associated antigen 1 (LFA-1), very late activation antigen 4 (VLA-4), Mac-1 (CD18/CD11b), and gp 150,95 (CD18/CD11c). Clinical and biochemical parameters of inflammation in the patients, as well as the duration of previous corticosteroid treatment, were prospectively recorded. Constitutive (PECAM-1, ICAM-1, ICAM-2, and P-selectin) and inducible (E-selectin and VCAM-1) endothelial adhesion molecules for leukocytes were mainly expressed by adventitial microvessels and neovessels within inflammatory infiltrates. Concurrent analysis of leukocyte receptors indicated a preferential use of VLA-4/VCAM-1 and LFA-1/ICAM-1 at the adventitia and Mac-1/ICAM-1 at the intima-media junction. The intensity of inducible endothelial adhesion molecule expression (E-selectin and VCAM-1) correlated with the intensity of the systemic inflammatory response. Previous corticosteroid treatment reduced, but did not completely abrogate, the expression of the inducible endothelial adhesion molecules E-selectin and VCAM-1. Inflammation-induced angiogenesis is the main site of leukocyte-endothelial cell interactions leading to the development of inflammatory infiltrates in GCA. The distribution of leukocyte-endothelial cell ligand pairs suggests a heterogeneity in leukocyte-endothelial cell interactions used by different functional cell subsets at distinct areas of the temporal artery.

  2. Molecular characterization of the gerbil C5a receptor and identification of a transmembrane domain V amino acid that is crucial for small molecule antagonist interaction.

    Science.gov (United States)

    Waters, Stephen M; Brodbeck, Robbin M; Steflik, Jeremy; Yu, Jianying; Baltazar, Carolyn; Peck, Amy E; Severance, Daniel; Zhang, Lu Yan; Currie, Kevin; Chenard, Bertrand L; Hutchison, Alan J; Maynard, George; Krause, James E

    2005-12-09

    Anaphylatoxin C5a is a potent inflammatory mediator associated with pathogenesis and progression of several inflammation-associated disorders. Small molecule C5a receptor (C5aR) antagonist development is hampered by species-specific receptor biology and the associated inability to use standard rat and mouse in vivo models. Gerbil is one rodent species reportedly responsive to small molecule C5aR antagonists with human C5aR affinity. We report the identification of the gerbil C5aR cDNA using a degenerate primer PCR cloning strategy. The nucleotide sequence revealed an open reading frame encoding a 347-amino acid protein. The cloned receptor (expressed in Sf9 cells) bound recombinant human C5a with nanomolar affinity. Alignment of the gerbil C5aR sequence with those from other species showed that a Trp residue in transmembrane domain V is the only transmembrane domain amino acid unique to small molecule C5aR antagonist-responsive species (i.e. gerbil, human, and non-human primate). Site-directed mutagenesis was used to generate human and mouse C5aRs with a residue exchange of this Trp residue. Mutation of Trp to Leu in human C5aR completely eliminated small molecule antagonist-receptor interaction. In contrast, mutation of Leu to Trp in mouse C5aR enabled small molecule antagonist-receptor interaction. This crucial Trp residue is located deeper within transmembrane domain V than residues reportedly involved in C5a- and cyclic peptide C5a antagonist-receptor interaction, suggesting a novel interaction site(s) for small molecule antagonists. These data provide insight into the basis for small molecule antagonist species selectivity and further define sites critical for C5aR activation and function.

  3. Interaction between H2O, N2, CO, NO, NO2 and N2O molecules and a defective WSe2 monolayer.

    Science.gov (United States)

    Ma, Dongwei; Ma, Benyuan; Lu, Zhiwen; He, Chaozheng; Tang, Yanan; Lu, Zhansheng; Yang, Zongxian

    2017-10-04

    In this study, the interaction between gas molecules, including H 2 O, N 2 , CO, NO, NO 2 and N 2 O, and a WSe 2 monolayer containing an Se vacancy (denoted as V Se ) has been theoretically studied. Theoretical results show that H 2 O and N 2 molecules are highly prone to be physisorbed on the V Se surface. The presence of the Se vacancy can significantly enhance the sensing ability of the WSe 2 monolayer toward H 2 O and N 2 molecules. In contrast, CO and NO molecules highly prefer to be molecularly chemisorbed on the V Se surface with the non-oxygen atom occupying the Se vacancy site. Furthermore, the exposed O atoms of the molecularly chemisorbed CO or NO can react with additional CO or NO molecules, to produce C-doped or N-doped WSe 2 monolayers. The calculated energies suggest that the filling of the CO or NO molecule and the removal of the exposed O atom are both energetically and dynamically favorable. Electronic structure calculations show that the WSe 2 monolayers are p-doped by the CO and NO molecules, as well as the C and N atoms. However, only the NO molecule and N atom doped WSe 2 monolayers exhibit significantly improved electronic structures compared with V Se . The NO 2 and N 2 O molecules will dissociate directly to form an O-doped WSe 2 monolayer, for which the defect levels due to the Se vacancy can be completely removed. The calculated energies suggest that although the dissociation processes for NO 2 and N 2 O molecules are highly exothermic, the N 2 O dissociation may need to operate at an elevated temperature compared with room temperature, due to its large energy barrier of ∼1 eV.

  4. Equipartition of energy in a one-dimensional model of diatomic molecules. III. Soft-interaction case

    International Nuclear Information System (INIS)

    Erpenbeck, J.J.; Cohen, E.G.D.

    1991-01-01

    The model of a one-dimensional, diatomic gas with harmonic intramolecular forces and soft intermolecular forces, introduced by Benettin, Galgani, and Giorgilli [Phys. Lett. A 120, 23 (1987)], is studied numerically for a set of initial conditions for various values of the vibrational frequency ω and the number of molecules N. The use of many trajectories, rather than a single one, as was done before, allows us to infer conclusions about the structure of the phase space of the system using statistical analysis of simple functions of the phase. Thus, for fixed ω and small N, the average vibrational energy differs from trajectory to trajectory, implying nonergodic behavior. However, these differences become statistically insignificant for large N, implying a transition to ergodicity. While this transition is not sharp, it occurs at larger N for increasing ω, due to the increasingly difficult exchange of energy between vibrational and translational degrees of freedom. The phase-space-averaged vibrational-energy time-autocorrelation function decays on two time scales for all frequencies considered, at least for N large enough that the system behaves ergodically. A rapid, Gaussian decay on the time scale of the mean free time is followed by a much slower, approximately stretched-exponential decay, due to interactions with adiabatic islands in phase space. This second time scale increases sharply with ω and is related to the increasingly slow, possibly Arnold-like, diffusion in phase space

  5. Interaction research on an antiviral molecule that targets the coat protein of southern rice black-streaked dwarf virus.

    Science.gov (United States)

    Ran, Longlu; Ding, Yan; Luo, Liangzhi; Gan, Xiuhai; Li, Xiangyang; Chen, Yongzhong; Hu, Deyu; Song, Baoan

    2017-10-01

    Southern rice black-streaked dwarf virus (SRBSDV) coat protein (P10) is the key protein required for viral transmission and host plant infection and is thus a promising target for anti-SRBSDV agent screening. In this study, P10 was obtained from Escherichia coli through cloning, expression, and purification. The antiviral agent Ningnanmycin was selected as control, and a series of antiviral compounds based on the structural scaffold of ferulic acid were analyzed. Size-exclusion chromatography analysis results showed that compound F27 can alter the aggregation of P10 proteins. Furthermore, fluorescence titration and microscale thermophoresis assay results indicated that F27 binds to P10 with K A of 5.75×10 5 M -1 and K D of 7.81μM. The ligand- and receptor-based three-dimensional quantitative structure-activity analyses were performed to determine the requirements for the interaction between the carboxyl structures and P10s. On the basis of the obtained models and information, we provided insights regarding the design and optimization of novel molecules as anti-SRBSDV agents. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Zirconium-based conversion film formation on zinc, aluminium and magnesium oxides and their interactions with functionalized molecules

    Science.gov (United States)

    Fockaert, L. I.; Taheri, P.; Abrahami, S. T.; Boelen, B.; Terryn, H.; Mol, J. M. C.

    2017-11-01

    Zirconium-based conversion treatment of zinc, aluminium and magnesium oxides have been studied in-situ using ATR-FTIR in a Kretschmann geometry. This set-up was coupled to an electrochemical cell, which allowed to obtain chemical and electrochemical information simultaneously as a function of conversion time. This elucidated the strong relation between physico-chemical surface properties and zirconium-based conversion kinetics. Whereas the surface hydroxyl density of zinc and aluminium increased during conversion, magnesium (hydr)oxide was shown to dissolve in the acid solution. Due to this dissolution, strong surface alkalization can be expected, explaining the rapid conversion kinetics. AES depth profiling was used to determine the final oxide thickness and elemental composition. This confirmed that magnesium is most active and forms a zirconium oxide layer approximately 10 times thicker than zinc. On the other hand, the presence of zirconium oxide on aluminium is very low and can be considered as not fully covering the metal oxide. Additionally, the converted oxide chemistry was related to the bonding mechanisms of amide functionalized molecules using ATR-FTIR and XPS. It was shown that inclusion of zirconium altered the acid-base properties, increasing the substrate proton donating capabilities in case of magnesium oxide and increasing hydrogen bonding and Bronsted interactions due to increased surface hydroxide fractions on zinc and aluminium substrates.

  7. Competitive Brownian and Lévy walkers

    Science.gov (United States)

    Heinsalu, E.; Hernández-García, E.; López, C.

    2012-04-01

    Population dynamics of individuals undergoing birth and death and diffusing by short- or long-range two-dimensional spatial excursions (Gaussian jumps or Lévy flights) is studied. Competitive interactions are considered in a global case, in which birth and death rates are influenced by all individuals in the system, and in a nonlocal but finite-range case in which interaction affects individuals in a neighborhood (we also address the noninteracting case). In the global case one single or few-cluster configurations are achieved with the spatial distribution of the bugs tied to the type of diffusion. In the Lévy case long tails appear for some properties characterizing the shape and dynamics of clusters. Under nonlocal finite-range interactions periodic patterns appear with periodicity set by the interaction range. This length acts as a cutoff limiting the influence of the long Lévy jumps, so that spatial configurations under the two types of diffusion become more similar. By dividing initially everyone into different families and following their descent it is possible to show that mixing of families and their competition is greatly influenced by the spatial dynamics.

  8. Electronic structure of CoPc adsorbed on Ag(100): Evidence for molecule-substrate interaction mediated by Co 3d orbitals

    Czech Academy of Sciences Publication Activity Database

    Salomon, E.; Amsalem, P.; Marom, N.; Vondráček, Martin; Kronik, L.; Koch, N.; Angot, T.

    2013-01-01

    Roč. 87, č. 7 (2013), "075407-1"-"075407-9" ISSN 1098-0121 R&D Projects: GA MŠk(CZ) LG12003 Institutional support: RVO:68378271 Keywords : cobalt-phthalocyanine * molecule-substrate interaction * photoemission spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013

  9. Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

    Science.gov (United States)

    Cole, Daniel J; Janecek, Matej; Stokes, Jamie E; Rossmann, Maxim; Faver, John C; McKenzie, Grahame J; Venkitaraman, Ashok R; Hyvönen, Marko; Spring, David R; Huggins, David J; Jorgensen, William L

    2017-08-17

    Free energy perturbation theory, in combination with enhanced sampling of protein-ligand binding modes, is evaluated in the context of fragment-based drug design, and used to design two new small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

  10. Brownian motion model with stochastic parameters for asset prices

    Science.gov (United States)

    Ching, Soo Huei; Hin, Pooi Ah

    2013-09-01

    The Brownian motion model may not be a completely realistic model for asset prices because in real asset prices the drift μ and volatility σ may change over time. Presently we consider a model in which the parameter x = (μ,σ) is such that its value x (t + Δt) at a short time Δt ahead of the present time t depends on the value of the asset price at time t + Δt as well as the present parameter value x(t) and m-1 other parameter values before time t via a conditional distribution. The Malaysian stock prices are used to compare the performance of the Brownian motion model with fixed parameter with that of the model with stochastic parameter.

  11. Human behavioral regularity, fractional Brownian motion, and exotic phase transition

    Science.gov (United States)

    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.

  12. On some possible generalizations of fractional Brownian motion

    Science.gov (United States)

    Lim, S. C.; Muniandy, S. V.

    2000-02-01

    Fractional Brownian motion (fBm) can be generalized to multifractional Brownian motion (mBm) if the Hurst exponent H is replaced by a deterministic function H( t). The two possible generalizations of mBm based on the moving average representation and the harmonizable representation are first shown to be equivalent up to a multiplicative deterministic function of time by Cohen [S. Cohen, in: M. Dekking et al. (Eds.), Fractals: Theory and Applications in Engineering, Springer, Berlin, 1999, p. 3.] using the Fourier transform method. In this Letter, we give an alternative verification of such an equivalence based on the direct computation of the covariances of these two Gaussian processes. There also exists another equivalent representation of mBm, which is a variant version of the harmonizable representation. Finally, we consider a generalization based on the Riemann-Liouville fractional integral, and study the large time asymptotic properties of this version of mBm.

  13. Fractional Brownian Motion:. Theory and Application to DNA Walk

    Science.gov (United States)

    Lim, S. C.; Muniandy, S. V.

    2001-09-01

    This paper briefly reviews the theory of fractional Brownian motion (FBM) and its generalization to multifractional Brownian motion (MBM). FBM and MBM are applied to a biological system namely the DNA sequence. By considering a DNA sequence as a fractal random walk, it is possible to model the noncoding sequence of human retinoblastoma DNA as a discrete version of FBM. The average scaling exponent or Hurst exponent of the DNA walk is estimated to be H = 0.60 ± 0.05 using the monofractal R/S analysis. This implies that the mean square fluctuation of DNA walk belongs to anomalous superdiffusion type. We also show that the DNA landscape is not monofractal, instead one has multifractal DNA landscape. The empirical estimates of the Hurst exponent falls approximately within the range H ~ 0.62 - 0.72. We propose two multifractal models, namely the MBM and multiscale FBM to describe the existence of different Hurst exponents in DNA walk.

  14. Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics

    KAUST Repository

    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.

  15. The Glassy Phase of Complex Branching Brownian Motion

    Science.gov (United States)

    Madaule, Thomas; Rhodes, Rémi; Vargas, Vincent

    2015-03-01

    In this paper, we study complex valued branching Brownian motion in the so-called glassy phase, also called phase II. In this context, we prove a limit theorem for the complex partition function hence confirming a conjecture formulated by Lacoin and the last two authors in a previous paper on complex Gaussian multiplicative chaos. We will show that the limiting partition function can be expressed as a product of a Gaussian random variable, mainly due to the windings of the phase, and a stable transform of the so-called derivative martingale, mainly due to the clustering of the modulus. The proof relies on the fine description of the extremal process available in the branching Brownian motion context.

  16. Exact master equation for a noncommutative Brownian particle

    International Nuclear Information System (INIS)

    Costa Dias, Nuno; Nuno Prata, Joao

    2009-01-01

    We derive the Hu-Paz-Zhang master equation for a Brownian particle linearly coupled to a bath of harmonic oscillators on the plane with spatial noncommutativity. The results obtained are exact to all orders in the noncommutative parameter. As a by-product we derive some miscellaneous results such as the equilibrium Wigner distribution for the reservoir of noncommutative oscillators, the weak coupling limit of the master equation and a set of sufficient conditions for strict purity decrease of the Brownian particle. Finally, we consider a high-temperature Ohmic model and obtain an estimate for the time scale of the transition from noncommutative to ordinary quantum mechanics. This scale is considerably smaller than the decoherence scale

  17. Interaction of slow electrons with high-pressure gases (Quasi-liquids). Synthesis of our knowledge on slow electron-molecule interactions. Progress report for year ending June 15, 1984

    International Nuclear Information System (INIS)

    McCorkle, D.L.; Christophorou, L.G.

    1984-01-01

    A crucial step in efforts to develop not only a coherent picture of radiation interaction with matter, but also to understand radiation effects and mechanisms, as well as the effects of chemical pollutants and toxic compounds, is to relate the often abundant knowledge on isolated molecules (low pressure gases) to that on liquids or solids. To understand the roles of the physical and chemical properties of molecules in biological reactions, the way these isolated-molecule properties change as molecules are embedded in gradually thicker and thicker (denser and denser) gaseous and, finally, liquid environments must be known. The work reported here, carried out both at the Physics Department of the University of Tennessee and at the Oak Ridge National Laboratory addresses itself to this question. At both places, high pressure (40 to approx. 8000 kPa) electron swarm experiments are currently in operation yielding the first information as to the effects of the density and nature of the environment on fundamental electron-molecule interaction processes at densities intermediate to those corresponding to low pressure gases and liquids, and the gradual transition from isolated molecule to condensed phase behavior. Basic physical data on the electronic states of atmospheric halocarbons in general, and of polycyclic aromatic hydrocarbons in particular were also studied. Such data are of special significance because of the occurrence of these molecules in the atmosphere, and are presently lacking

  18. Adiabatic Processes Realized with a Trapped Brownian Particle

    Science.gov (United States)

    Martínez, Ignacio A.; Roldán, Édgar; Dinis, Luis; Petrov, Dmitri; Rica, Raúl A.

    2015-03-01

    The ability to implement adiabatic processes in the mesoscale is of key importance in the study of artificial or biological micro- and nanoengines. Microadiabatic processes have been elusive to experimental implementation due to the difficulty in isolating Brownian particles from their fluctuating environment. Here we report on the experimental realization of a microscopic quasistatic adiabatic process employing a trapped Brownian particle. We circumvent the complete isolation of the Brownian particle by designing a protocol where both characteristic volume and temperature of the system are changed in such a way that the entropy of the system is conserved along the process. We compare the protocols that follow from either the overdamped or underdamped descriptions, demonstrating that the latter is mandatory in order to obtain a vanishing average heat flux to the particle. We provide analytical expressions for the distributions of the fluctuating heat and entropy and verify them experimentally. Our protocols could serve to implement the first microscopic engine that is able to attain the fundamental limit for the efficiency set by Carnot.

  19. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

    Science.gov (United States)

    Benedetti, Fabrizio; Japaridze, Aleksandre; Dorier, Julien; Racko, Dusan; Kwapich, Robert; Burnier, Yannis; Dietler, Giovanni; Stasiak, Andrzej

    2015-01-01

    DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA–DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes. PMID:25653164

  20. Novel secreted isoform of adhesion molecule ICAM-4: Potential regulator of membrane-associated ICAM-4 interactions

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Gloria; Spring, Frances A.; Parons, Stephen F.; Mankelow, Tosti J.; Peters, Luanne L.; Koury, Mark J.; Mohandas, Narla; Anstee, David J.; Chasis, Joel Anne

    2003-02-18

    ICAM-4, a newly characterized adhesion molecule, is expressed early in human erythropoiesis and functions as a ligand for binding a4b1 and aV integrin-expressing cells. Within the bone marrow, erythroblasts surround central macrophages forming erythroblastic islands. Evidence suggests that these islands are highly specialized subcompartments where cell adhesion events, in concert with cytokines, play critical roles in regulating erythropoiesis and apoptosis. Since erythroblasts express a4b1 and ICAM-4 and macrophages exhibit aV, ICAM-4 is an attractive candidate for mediating cellular interactions within erythroblastic islands. To determine whether ICAM-4 binding properties are conserved across species, we first cloned and sequenced the murine homologue. The translated amino acid sequence showed 68 percent overall identity with human ICAM-4. Using recombinant murine ICAM-4 extracellular domains, we discovered that hematopoietic a4b1-expressing HEL cells and non-hematopoietic aV-expressing FLY cells adhered to mouse ICAM-4. Cell adhesion studies showed that FLY and HEL cells bound to mouse and human proteins with similar avidity. These data strongly suggest conservation of integrin-binding properties across species. Importantly, we characterized a novel second splice cDNA that would be predicted to encode an ICAM-4 isoform, lacking the membrane-spanning domain. Erythroblasts express both isoforms of ICAM-4. COS-7 cells transfected with GFP constructs of prototypic or novel ICAM-4 cDNA showed different cellular localization patterns. Moreover, analysis of tissue culture medium revealed that the novel ICAM-4 cDNA encodes a secreted protein. We postulate that secretion of this newly described isoform, ICAM-4S, may modulate binding of membrane-associated ICAM-4 and could thus play a critical regulatory role in erythroblast molecular attachments.

  1. Quantum Drude oscillator model of atoms and molecules: Many-body polarization and dispersion interactions for atomistic simulation

    Science.gov (United States)

    Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.

    2013-04-01

    Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.

  2. Early-stage evolution of particle size distribution with Johnson's SB function due to Brownian coagulation

    International Nuclear Information System (INIS)

    Tang Hong; Lin Jianzhong

    2013-01-01

    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 S B 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 S B function as the general distribution function. And then, the time evolution of particle size distributions using the Johnson's S B function as the initial distribution can be obtained by several lower order moment equations of the Johnson's S B 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 S B function has the ability of describing the early time evolution of different initial particle size distributions. (paper)

  3. Free molecule flow analysis of the interaction of skimming hardware components and background gas with free jets

    International Nuclear Information System (INIS)

    Raghuraman, P.; Bossel, U.

    1974-01-01

    Under conditions typical for the extraction of nozzle beams from free jets the rarefied flow pattern in the expansion chamber containing skimming hardware components and background gas is studied using a free molecule solution to the Boltzmann equation

  4. INTERACTION OF LASER RADIATION WITH MATTER: Effect of stimulated emission on the distribution of CO molecules over vibrational levels

    Science.gov (United States)

    Grigorian, G. M.; Kochetov, I. V.

    2008-10-01

    The vibrational distribution function (VDF) of CO molecules is measured in the presence and absence of generation in a CO laser pumped by a longitudinal dc discharge. Kinetic equations for the VDF and the Boltzmann equation for the energy distribution function of electrons are solved simultaneously in a theoretical model. A comparison of the experimental and calculated lasing spectra and VDF demonstrates their good agreement. By introducing an absorbing cell with different gases (NO, C2H4, CO2, C6H6) into a resonator, the influence of selection of laser lines on the lasing spectrum and the VDF of CO molecules is studied. It is shown experimentally that the population of CO molecules at vibrational levels involved in lasing and at higher levels strongly decreases and the VDF at lower levels changes insignificantly. It is demonstrated that the VDF shape of CO molecules at high vibrational levels can be changed by introducing intracavity absorption.

  5. Effect of conformational propensity of peptide antigens in their interaction with MHC class II molecules. Failure to document the importance of regular secondary structures

    DEFF Research Database (Denmark)

    Sette, A; Lamont, A; Buus, S

    1989-01-01

    In an attempt to define some of the conformational requirements for binding of the antigenic peptide OVA 323-336 to purified IAd molecules, three distinct experimental approaches were applied. First, the effect of introducing proline or glycine residues within the region of OVA 323-336 crucial...... for its IAd binding capacity was analyzed. In most instances these substitutions had little or no effect, suggesting that neither alpha-helical nor beta-sheet regular structures may be strictly required for productive interaction with MHC molecules. Some of the same substitutions were also found to have...... no effect on the capacity of the peptide to stimulate OVA 323-336 specific T cell hybridomas, suggesting that regular structures such as alpha-helices or beta-sheets may not be strictly required for T cell stimulation, either. Second, we introduced, within the OVA 323-336 molecule, structural modifications...

  6. Single-molecule study of molecular mobility in the cytoplasm of Escherichia coli

    Science.gov (United States)

    Lill, Yoriko; Kaserer, Wallace A.; Newton, Salete M.; Lill, Markus; Klebba, Phillip E.; Ritchie, Ken

    2012-08-01

    The cytoplasm of bacterial cells is filled with individual molecules and molecular complexes that rely on diffusion to bring them together for interaction. The mobility of molecules in the cytoplasm has been characterized by several techniques mainly using fluorescent probes and ensemble methods. In order to probe the microenvrionment inside the cytoplasm as viewed by an individual molecule, we have studied single green fluorescent proteins (GFPs) diffusing in the cytoplasm of Escherichia coli cells at observation at rates ranging from 60 to 1000 Hz. Over long times the diffusion shows confinement due to the geometry of the cells themselves. A simulation in model cells using the actual distribution of cell sizes found in the experiments describes accurately the experimental results as well as reveals a short time diffusion coefficient that agrees well with that determined by ensemble methods. Higher short time diffusion coefficients can be obtained by filling the simulated cell with small spheres modeling cytoplasmic molecules and, depending on the density of particles included in the modeled cytoplasm, can approach the diffusion coefficient of GFPs found in water. Thus, single-molecule tracking combined with analysis using simple simulation of Brownian motion is able to reveal the main contributors to the GFP mobility in the cytoplasm of E. coli.

  7. Optimal fits of diffusion constants from single-time data points of Brownian trajectories.

    Science.gov (United States)

    Boyer, Denis; Dean, David S; Mejía-Monasterio, Carlos; Oshanin, Gleb

    2012-12-01

    Experimental methods based on single particle tracking (SPT) are being increasingly employed in the physical and biological sciences, where nanoscale objects are visualized with high temporal and spatial resolution. SPT can probe interactions between a particle and its environment but the price to be paid is the absence of ensemble averaging and a consequent lack of statistics. Here we address the benchmark question of how to accurately extract the diffusion constant of one single Brownian trajectory. We analyze a class of estimators based on weighted functionals of the square displacement. For a certain choice of the weight function these functionals provide the true ensemble averaged diffusion coefficient, with a precision that increases with the trajectory resolution.

  8. Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

    Science.gov (United States)

    Duan, Zhao-Wen; Li, Wei; Xie, Ping; Dou, Shuo-Xing; Wang, Peng-Ye

    2010-04-01

    Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking" interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

  9. Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

    International Nuclear Information System (INIS)

    Zhao-Wen, Duan; Wei, Li; Ping, Xie; Shuo-Xing, Dou; Peng-Ye, Wang

    2010-01-01

    Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking” interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon. (cross-disciplinary physics and related areas of science and technology)

  10. Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling.

    Science.gov (United States)

    Huang, Yu-Ming M; Huber, Gary A; Wang, Nuo; Minteer, Shelley D; McCammon, J Andrew

    2018-02-01

    Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH-CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH-CS metabolons that have different structural orientations in their complexes. Three MDH-CS metabolons from native bovine, wild-type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild-type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another. © 2017 The Protein Society.

  11. Scanning near-field optical microscopy-based study of local dynamics of receptor-ligand interactions at the single molecule level

    Science.gov (United States)

    Mensi, M.; Dukenbayev, K.; Sekatskii, S. K.; Dietler, G.

    2010-01-01

    A scanning near-field optical microscope (SNOM)—based modification of the method to study the dynamics of single molecule receptor—ligand interactions exploiting the fluorescence imaging by total internal reflection fluorescence microscopy is introduced. The main advantage of this approach consists in the possibility to study the single molecule interaction dynamics with a subwavelength spatial resolution and a submillisecond time resolution. Additionally, due to the much smaller irradiation area and some other technical features, such a modification enables to enlarge the scope of the receptor—ligand pairs to be investigated and to improve the temporal resolution. We briefly discuss corresponding experimental set up with a special accent on the SNOM operation in liquid and present some preliminary results of related investigations.

  12. ISOLATED MOLECULES IN METALS

    NARCIS (Netherlands)

    1992-01-01

    In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.

  13. Quantum electrodynamics with nonrelativistic sources. V. Electromagnetic field correlations and intermolecular interactions between molecules in either ground or excited states

    International Nuclear Information System (INIS)

    Power, E.A.; Thirunamachandran, T.

    1993-01-01

    Spatial correlations between electromagnetic fields arising from neutral sources with electric-dipole transition moments are calculated using nonrelativistic quantum electrodynamics in the multipolar formalism. Expressions for electric-electric, magnetic-magnetic, and electric-magnetic correlation functions at two points r and r' are given for a source molecule in either a ground or an excited state. In contrast to the electric-electric and magnetic-magnetic cases there are no electric-magnetic correlations for a ground-state molecule. For an excited molecule the downward transitions contribute additional terms which have modulating factors depending on (r-r')/λ. From these correlation functions electric and magnetic energy densities are found by setting r=r'. These energy densities are then used in a response formalism to calculate intermolecular energy shifts. In the case of two ground-state molecules this leads to the Casimir-Polder potential. However, for a pair of molecules, one or both excited, there are additional terms arising from downward transitions. An important feature of these energies is that they exhibit an R -2 dependence for large intermolecular separations R. This dependence is interpreted in terms of the Poynting vector, which itself can be obtained by setting r=r' in the electric-magnetic correlation function

  14. Hypercrosslinked large surface area porous polymer monoliths for hydrophilic interaction liquid chromatography of small molecules featuring zwitterionic functionalities attached to gold nanoparticles held in layered structure

    OpenAIRE

    Lv, Yongqin; Lin, Zhixing; Svec, Frantisek

    2012-01-01

    A novel approach to porous polymer monoliths hypercrosslinked to obtain large surface areas and modified with zwitterionic functionalities through the attachment of gold nanoparticles in a layered architecture has been developed. The capillary columns were used for the separation of small molecules in hydrophilic interaction liquid chromatography mode. First, a monolith with a very large surface area of 430 m2/g was prepared by hypercrosslinking from a generic poly(4-methylstyrene-co-vinylben...

  15. Parameter inference from hitting times for perturbed Brownian motion

    DEFF Research Database (Denmark)

    Tamborrino, Massimiliano; Ditlevsen, Susanne; Lansky, Peter

    2015-01-01

    ? To answer this question we describe the effect of the intervention through parameter changes of the law governing the internal process. Then, the time interval between the start of the process and the final event is divided into two subintervals: the time from the start to the instant of intervention...... from observations of S and R and compare them statistically? Maximum likelihood estimators are calculated and applied on simulated data under the assumption that the process before and after the intervention is described by the same type of model, i.e. a Brownian motion, but with different parameters...

  16. 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......-based approach, the potential of BSS processes to model turbulent velocity time series. It turns out that this family of processes reproduces accurately some of the main features present in turbulent time series, such as the distribution of the velocity increments and the statistics of the Kolmogorov variable...

  17. Pricing geometric Asian rainbow options under fractional Brownian motion

    Science.gov (United States)

    Wang, Lu; Zhang, Rong; Yang, Lin; Su, Yang; Ma, Feng

    2018-03-01

    In this paper, we explore the pricing of the assets of Asian rainbow options under the condition that the assets have self-similar and long-range dependence characteristics. Based on the principle of no arbitrage, stochastic differential equation, and partial differential equation, we obtain the pricing formula for two-asset rainbow options under fractional Brownian motion. Next, our Monte Carlo simulation experiments show that the derived pricing formula is accurate and effective. Finally, our sensitivity analysis of the influence of important parameters, such as the risk-free rate, Hurst exponent, and correlation coefficient, on the prices of Asian rainbow options further illustrate the rationality of our pricing model.

  18. Treadmilling of actin filaments via Brownian dynamics simulations

    DEFF Research Database (Denmark)

    Guo, Kunkun; Shillcock, Julian C.; Lipowsky, Reinhard

    2010-01-01

    Actin polymerization is coupled to the hydrolysis of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and inorganic phosphate (Pi). Therefore, each protomer within an actin filament can attain three different nucleotide states corresponding to bound ATP, ADP / Pi, and ADP....... These protomer states form spatial patterns on the growing (or shrinking) filaments. Using Brownian dynamics simulations, the growth behavior of long filaments is studied, together with the associated protomer patterns, as a function of ATP-actin monomer concentration, CT, within the surrounding solution...

  19. Moments of inertia and the shapes of Brownian paths

    International Nuclear Information System (INIS)

    Fougere, F.; Desbois, J.

    1993-01-01

    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

  20. Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

    KAUST Repository

    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.

  1. Permutation entropy of fractional Brownian motion and fractional Gaussian noise

    International Nuclear Information System (INIS)

    Zunino, L.; Perez, D.G.; Martin, M.T.; Garavaglia, M.; Plastino, A.; Rosso, O.A.

    2008-01-01

    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

  2. Brownian motion of a dust particle in a plasma

    Energy Technology Data Exchange (ETDEWEB)

    Mendonca, J.T.; Shukla, P.K.; Martins, A.M.; Guerra, R. [Grupo de Lasers e Plasmas (GOLP)/Centro de Electrodinamica, Instituto Superior Tecnico, 1096 Lisboa Codex (Portugal)

    1997-03-01

    A new version of the Brownian motion describing the motion of a dust particle in a turbulent plasma is considered. Here, the stochastic force acting on the dust particle is due to the fluctuations of the plasma potential and not due to the usual molecular collisions. Another significant difference is due to the fact that the dust electric charge is not constant but fluctuates with the potential. A four-dimensional formulation of the problem is also given. {copyright} {ital 1997 American Institute of Physics.}

  3. Random functions via Dyson Brownian Motion: progress and problems

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Gaoyuan; Battefeld, Thorsten [Institute for Astrophysics, University of Goettingen,Friedrich Hund Platz 1, D-37077 Goettingen (Germany)

    2016-09-05

    We develope a computationally efficient extension of the Dyson Brownian Motion (DBM) algorithm to generate random function in C{sup 2} locally. We further explain that random functions generated via DBM show an unstable growth as the traversed distance increases. This feature restricts the use of such functions considerably if they are to be used to model globally defined ones. The latter is the case if one uses random functions to model landscapes in string theory. We provide a concrete example, based on a simple axionic potential often used in cosmology, to highlight this problem and also offer an ad hoc modification of DBM that suppresses this growth to some degree.

  4. Ellipsoidal Brownian self-driven particles in a magnetic field

    Science.gov (United States)

    Sandoval, Mario; Wai-Tong, Fan; Shun Pak, On

    We study the two-dimensional Brownian dynamics of an ellipsoidal paramagnetic microswimmer moving at low Reynolds number and subject to a magnetic field. Its corresponding mean-square displacement showing the effect of particles's shape, activity, and magnetic field on the microswimmer's diffusion is analytically obtained. A comparison among analytical and computational results is also made and we obtain good agreement. Additionally, the effect of self-propulsion on the transition time from anisotropic to isotropic diffusion of the ellipse is also elucidated. CONACYT GRANT: CB 2014/237848.

  5. Importance of Rigidity in Designing Small Molecule Drugs To Tackle Protein-Protein Interactions (PPIs) through Stabilization of Desired Conformers.

    Science.gov (United States)

    Lawson, Alastair D G; MacCoss, Malcolm; Heer, Jag P

    2017-11-28

    Tackling PPIs, particularly by stabilizing clinically favored conformations of target proteins, with orally available, bona fide small molecules remains a significant but immensely worthwhile challenge for the pharmaceutical industry. Success may be more likely through the application of nature's learnings to build intrinsic rigidity into the design of clinical candidates.

  6. Quantum chemical investigation of the interaction between a hydrogen molecule and a solid surface using the partitioning technique

    International Nuclear Information System (INIS)

    Kuenne, L.D.

    1984-01-01

    The partitioning technique is used to investigate the chemisorption of hydrogen. Including non-zero overlap between atomic orbitals the developed formulation of the problem is valid in any LCAO-approximation. Its extension to the problem of chemisorption of other molecules is briefly discussed. (author)

  7. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: potential and limitations.

    Science.gov (United States)

    Cottier, Stéphanie; Mönig, Timon; Wang, Zheming; Svoboda, Jiří; Boland, Wilhelm; Kaiser, Markus; Kombrink, Erich

    2011-01-01

    Chemical genetics is a powerful scientific strategy that utilizes small bioactive molecules as experimental tools to unravel biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that can be used to dissect functions of biological systems. Once the bioactivity of a natural or synthetic compound has been critically evaluated the challenge remains to identify its molecular target and mode of action, which usually is a time-consuming and labor-intensive process. To facilitate this task, we decided to implement the yeast three-hybrid (Y3H) technology as a general experimental platform to scan the whole Arabidopsis proteome for targets of small signaling molecules. The Y3H technology is based on the yeast two-hybrid system and allows direct cloning of proteins that interact in vivo with a synthetic hybrid ligand, which comprises the biologically active molecule of interest covalently linked to methotrexate (Mtx). In yeast nucleus the hybrid ligand connects two fusion proteins: the Mtx part binding to dihydrofolate reductase fused to a DNA-binding domain (encoded in the yeast strain), and the bioactive molecule part binding to its potential protein target fused to a DNA-activating domain (encoded on a cDNA expression vector). During cDNA library screening, the formation of this ternary, transcriptional activator complex leads to reporter gene activation in yeast cells, and thereby allows selection of the putative targets of small bioactive molecules of interest. Here we present the strategy and experimental details for construction and application of a Y3H platform, including chemical synthesis of different hybrid ligands, construction of suitable cDNA libraries, the choice of yeast strains, and appropriate screening conditions. Based on the results obtained and the current literature we discuss the perspectives and limitations of the Y3H approach for identifying targets of small bioactive molecules.

  8. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: Potential and limitations

    Directory of Open Access Journals (Sweden)

    Stéphanie eCottier

    2011-12-01

    Full Text Available Chemical genetics is a powerful scientific strategy that utilizes small bioactive molecules as experimental tools to unravel biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that can be used to dissect functions of biological systems. Once the bioactivity of a natural or synthetic compound has been critically evaluated the challenge remains to identify its molecular target and mode of action, which usually is a time consuming and labor-intensive process. To facilitate this task, we decided to implement the yeast three-hybrid (Y3H technology as a general experimental platform to scan the whole Arabidopsis proteome for targets of small signaling molecules. The Y3H technology is based on the yeast two-hybrid system and allows direct cloning of proteins that interact in vivo with a synthetic hybrid ligand, which comprises the biologically active molecule of interest covalently linked to methotrexate (Mtx. In yeast nucleus the hybrid ligand connects two fusion proteins: the Mtx part binding to dihydrofolate reductase fused to a DNA binding domain (encoded in the yeast strain, and the bioactive molecule part binding to its potential protein target fused to a DNA activating domain (encoded on a cDNA expression vector. During cDNA library screening, the formation of this ternary, transcriptional activator complex leads to reporter gene activation in yeast cells, and thereby allows selection of the putative targets of small bioactive molecules of interest. Here we present the strategy and experimental details for construction and application of a Y3H platform, including chemical synthesis of different hybrid ligands, construction of suitable cDNA libraries, the choice of yeast strains, and appropriate screening conditions. Based on the results obtained and the current literature we discussed the perspectives and limitations of the Y3H approach for identifying targets of small bioactive molecules.

  9. Brownian motion in a classical ideal gas: A microscopic approach to ...

    Indian Academy of Sciences (India)

    of a surface profile due to random deposition [10] are a few examples of such a situation and the description ... motion of the Brownian particle through an ideal gas to be a jump Markov process,. Gillespie [14] and van ... Brownian particle moving in an ideal gas at a fixed temperature, using a combi- nation of microscopic ...

  10. A Simplified Treatment of Brownian Motion and Stochastic Differential Equations Arising in Financial Mathematics

    Science.gov (United States)

    Parlar, Mahmut

    2004-01-01

    Brownian motion is an important stochastic process used in modelling the random evolution of stock prices. In their 1973 seminal paper--which led to the awarding of the 1997 Nobel prize in Economic Sciences--Fischer Black and Myron Scholes assumed that the random stock price process is described (i.e., generated) by Brownian motion. Despite its…

  11. Biased motion of a brownian particle for the pausing time behavior of the CTRW

    Energy Technology Data Exchange (ETDEWEB)

    Kim, K.S. (National Fisheries Univ., Busan (Republic of Korea))

    1982-12-01

    The purpose of this paper is to discuss the biased Brownian motion with the absorbing barrier for the pausing time behavior of the CTRW (continuous-time random walk method), regarding a Brownian particle as a walker. For two pausing time density functions, the respective values for the transport averaged velocity and the dispersion are calculated as the time t becomes large.

  12. Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

    International Nuclear Information System (INIS)

    Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.

    2011-01-01

    Highlights: → Molecular Dynamics codes implemented on GPUs have achieved two-order of magnitude computational accelerations. → Brownian Dynamics and Dissipative Particle Dynamics simulations require a large number of random numbers per time step. → We introduce a method for generating small batches of pseudorandom numbers distributed over many threads of calculations. → With this method, Dissipative Particle Dynamics is implemented on a GPU device without requiring thread-to-thread communication. - Abstract: Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.

  13. First passage Brownian functional properties of snowmelt dynamics

    Science.gov (United States)

    Dubey, Ashutosh; Bandyopadhyay, Malay

    2018-04-01

    In this paper, we model snow-melt dynamics in terms of a Brownian motion (BM) with purely time dependent drift and difusion and examine its first passage properties by suggesting and examining several Brownian functionals which characterize the lifetime and reactivity of such stochastic processes. We introduce several probability distribution functions (PDFs) associated with such time dependent BMs. For instance, for a BM with initial starting point x0, we derive analytical expressions for : (i) the PDF P(tf|x0) of the first passage time tf which specify the lifetime of such stochastic process, (ii) the PDF P(A|x0) of the area A till the first passage time and it provides us numerous valuable information about the total fresh water availability during melting, (iii) the PDF P(M) associated with the maximum size M of the BM process before the first passage time, and (iv) the joint PDF P(M; tm) of the maximum size M and its occurrence time tm before the first passage time. These P(M) and P(M; tm) are useful in determining the time of maximum fresh water availability and in calculating the total maximum amount of available fresh water. These PDFs are examined for the power law time dependent drift and diffusion which matches quite well with the available data of snowmelt dynamics.

  14. Three-dimensional nanoscale imaging by plasmonic Brownian microscopy

    Science.gov (United States)

    Labno, Anna; Gladden, Christopher; Kim, Jeongmin; Lu, Dylan; Yin, Xiaobo; Wang, Yuan; Liu, Zhaowei; Zhang, Xiang

    2017-12-01

    Three-dimensional (3D) imaging at the nanoscale is a key to understanding of nanomaterials and complex systems. While scanning probe microscopy (SPM) has been the workhorse of nanoscale metrology, its slow scanning speed by a single probe tip can limit the application of SPM to wide-field imaging of 3D complex nanostructures. Both electron microscopy and optical tomography allow 3D imaging, but are limited to the use in vacuum environment due to electron scattering and to optical resolution in micron scales, respectively. Here we demonstrate plasmonic Brownian microscopy (PBM) as a way to improve the imaging speed of SPM. Unlike photonic force microscopy where a single trapped particle is used for a serial scanning, PBM utilizes a massive number of plasmonic nanoparticles (NPs) under Brownian diffusion in solution to scan in parallel around the unlabeled sample object. The motion of NPs under an evanescent field is three-dimensionally localized to reconstruct the super-resolution topology of 3D dielectric objects. Our method allows high throughput imaging of complex 3D structures over a large field of view, even with internal structures such as cavities that cannot be accessed by conventional mechanical tips in SPM.

  15. Suspended particle transport through constriction channel with Brownian motion

    Science.gov (United States)

    Hanasaki, Itsuo; Walther, Jens H.

    2017-08-01

    It is well known that translocation events of a polymer or rod through pores or narrower parts of micro- and nanochannels have a stochastic nature due to the Brownian motion. However, it is not clear whether the objects of interest need to have a larger size than the entrance to exhibit the deviation from the dynamics of the surrounding fluid. We show by numerical analysis that the particle injection into the narrower part of the channel is affected by thermal fluctuation, where the particles have spherical symmetry and are smaller than the height of the constriction. The Péclet number (Pe) is the order parameter that governs the phenomena, which clarifies the spatio-temporal significance of Brownian motion compared to hydrodynamics. Furthermore, we find that there exists an optimal condition of Pe to attain the highest flow rate of particles relative to the dispersant fluid flow. Our finding is important in science and technology from nanopore DNA sequencers and lab-on-a-chip devices to filtration by porous materials and chromatography.

  16. 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.

  17. Intermittency and multifractional Brownian character of geomagnetic time series

    Science.gov (United States)

    Consolini, G.; De Marco, R.; De Michelis, P.

    2013-07-01

    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.

  18. Mathematical interpretation of Brownian motor model: Limit cycles and directed transport phenomena

    Science.gov (United States)

    Yang, Jianqiang; Ma, Hong; Zhong, Suchuang

    2018-03-01

    In this article, we first suggest that the attractor of Brownian motor model is one of the reasons for the directed transport phenomenon of Brownian particle. We take the classical Smoluchowski-Feynman (SF) ratchet model as an example to investigate the relationship between limit cycles and directed transport phenomenon of the Brownian particle. We study the existence and variation rule of limit cycles of SF ratchet model at changing parameters through mathematical methods. The influences of these parameters on the directed transport phenomenon of a Brownian particle are then analyzed through numerical simulations. Reasonable mathematical explanations for the directed transport phenomenon of Brownian particle in SF ratchet model are also formulated on the basis of the existence and variation rule of the limit cycles and numerical simulations. These mathematical explanations provide a theoretical basis for applying these theories in physics, biology, chemistry, and engineering.

  19. Noninvasive penetration of 5 nm hyaluronic acid molecules across the epidermal barrier (in vitro) and its interaction with human skin cells.

    Science.gov (United States)

    Nashchekina, Yu A; Raydan, M

    2018-02-01

    Hyaluronic acid represents one of the major components of the extracellular environment. The main challenge remains in the ability to deliver these molecules noninvasively across the skin barrier, which can be overcome by the reduction in size to an extent that allows these molecules to pass across the skin barrier. The aim of this study was to measure the penetration and bioavailability of low molecular weight hyaluronic acid to cross an epidermal barrier model. Determining the quantity of hyaluronic acid in the test solutions was carried with method of photocolorimetry analysis. Investigation of the interaction of cells with LMWHA was studied with a confocal microscope. The study showed that LMWHA is able to cross the epidermis. Most effective penetration level is during the first 6 hours reaching 75%, and then the concentration started to decline and reached the equilibrium state within the following 2 hours. Confocal laser microscopy demonstrated different distribution and behavior of these molecules among the keratinocytes and fibroblasts. Reducing the size of hyaluronic acid to 5 nm enhance their transport across the epidermal layer. The concentration of hyaluronic acid molecules was higher on the fibroblast surface in comparison to their extracellular environment. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. System in biology leading to cell pathology: stable protein-protein interactions after covalent modifications by small molecules or in transgenic cells.

    Science.gov (United States)

    Malina, Halina Z

    2011-01-19

    The physiological processes in the cell are regulated by reversible, electrostatic protein-protein interactions. Apoptosis is such a regulated process, which is critically important in tissue homeostasis and development and leads to complete disintegration of the cell. Pathological apoptosis, a process similar to apoptosis, is associated with aging and infection. The current study shows that pathological apoptosis is a process caused by the covalent interactions between the signaling proteins, and a characteristic of this pathological network is the covalent binding of calmodulin to regulatory sequences. Small molecules able to bind covalently to the amino group of lysine, histidine, arginine, or glutamine modify the regulatory sequences of the proteins. The present study analyzed the interaction of calmodulin with the BH3 sequence of Bax, and the calmodulin-binding sequence of myristoylated alanine-rich C-kinase substrate in the presence of xanthurenic acid in primary retinal epithelium cell cultures and murine epithelial fibroblast cell lines transformed with SV40 (wild type [WT], Bid knockout [Bid-/-], and Bax-/-/Bak-/- double knockout [DKO]). Cell death was observed to be associated with the covalent binding of calmodulin, in parallel, to the regulatory sequences of proteins. Xanthurenic acid is known to activate caspase-3 in primary cell cultures, and the results showed that this activation is also observed in WT and Bid-/- cells, but not in DKO cells. However, DKO cells were not protected against death, but high rates of cell death occurred by detachment. The results showed that small molecules modify the basic amino acids in the regulatory sequences of proteins leading to covalent interactions between the modified sequences (e.g., calmodulin to calmodulin-binding sites). The formation of these polymers (aggregates) leads to an unregulated and, consequently, pathological protein network. The results suggest a mechanism for the involvement of small molecules

  1. Improved Limits on Axionlike-Particle-Mediated P , T -Violating Interactions between Electrons and Nucleons from Electric Dipole Moments of Atoms and Molecules

    Science.gov (United States)

    Stadnik, Y. V.; Dzuba, V. A.; Flambaum, V. V.

    2018-01-01

    In the presence of P , T -violating interactions, the exchange of axionlike particles between electrons and nucleons in atoms and molecules induces electric dipole moments (EDMs) of atoms and molecules. We perform calculations of such axion-exchange-induced atomic EDMs using the relativistic Hartree-Fock-Dirac method including electron core polarization corrections. We present analytical estimates to explain the dependence of these induced atomic EDMs on the axion mass and atomic parameters. From the experimental bounds on the EDMs of atoms and molecules, including Cs 133 , Tl 205 , Xe 129 , Hg 199 , Yb 171 F 19 , Hf 180 F+ 19 , and Th 232 O 16 , we constrain the P , T -violating scalar-pseudoscalar nucleon-electron and electron-electron interactions mediated by a generic axionlike particle of arbitrary mass. Our limits improve on existing laboratory bounds from other experiments by many orders of magnitude for ma≳10-2 eV . We also place constraints on C P violation in certain types of relaxion models.

  2. Ureaplasma diversum Genome Provides New Insights about the Interaction of the Surface Molecules of This Bacterium with the Host.

    Directory of Open Access Journals (Sweden)

    Lucas M Marques

    Full Text Available Whole genome sequencing and analyses of Ureaplasma diversum ATCC 49782 was undertaken as a step towards understanding U. diversum biology and pathogenicity. The complete genome showed 973,501 bp in a single circular chromosome, with 28.2% of G+C content. A total of 782 coding DNA sequences (CDSs, and 6 rRNA and 32 tRNA genes were predicted and annotated. The metabolic pathways are identical to other human ureaplasmas, including the production of ATP via hydrolysis of the urea. Genes related to pathogenicity, such as urease, phospholipase, hemolysin, and a Mycoplasma Ig binding protein (MIB-Mycoplasma Ig protease (MIP system were identified. More interestingly, a large number of genes (n = 40 encoding surface molecules were annotated in the genome (lipoproteins, multiple-banded antigen like protein, membrane nuclease lipoprotein and variable surface antigens lipoprotein. In addition, a gene encoding glycosyltransferase was also found. This enzyme has been associated with the production of capsule in mycoplasmas and ureaplasma. We then sought to detect the presence of a capsule in this organism. A polysaccharide capsule from 11 to 17 nm of U. diversum was observed trough electron microscopy and using specific dyes. This structure contained arabinose, xylose, mannose, galactose and glucose. In order to understand the inflammatory response against these surface molecules, we evaluated the response of murine macrophages J774 against viable and non-viable U. diversum. As with viable bacteria, non-viable bacteria were capable of promoting a significant inflammatory response by activation of Toll like receptor 2 (TLR2, indicating that surface molecules are important for the activation of inflammatory response. Furthermore, a cascade of genes related to the inflammasome pathway of macrophages was also up-regulated during infection with viable organisms when compared to non-infected cells. In conclusion, U. diversum has a typical ureaplasma genome and

  3. Ureaplasma diversum Genome Provides New Insights about the Interaction of the Surface Molecules of This Bacterium with the Host.

    Science.gov (United States)

    Marques, Lucas M; Rezende, Izadora S; Barbosa, Maysa S; Guimarães, Ana M S; Martins, Hellen B; Campos, Guilherme B; do Nascimento, Naíla C; Dos Santos, Andrea P; Amorim, Aline T; Santos, Verena M; Farias, Sávio T; Barrence, Fernanda  C; de Souza, Lauro M; Buzinhani, Melissa; Arana-Chavez, Victor E; Zenteno, Maria E; Amarante-Mendes, Gustavo P; Messick, Joanne B; Timenetsky, Jorge

    2016-01-01

    Whole genome sequencing and analyses of Ureaplasma diversum ATCC 49782 was undertaken as a step towards understanding U. diversum biology and pathogenicity. The complete genome showed 973,501 bp in a single circular chromosome, with 28.2% of G+C content. A total of 782 coding DNA sequences (CDSs), and 6 rRNA and 32 tRNA genes were predicted and annotated. The metabolic pathways are identical to other human ureaplasmas, including the production of ATP via hydrolysis of the urea. Genes related to pathogenicity, such as urease, phospholipase, hemolysin, and a Mycoplasma Ig binding protein (MIB)-Mycoplasma Ig protease (MIP) system were identified. More interestingly, a large number of genes (n = 40) encoding surface molecules were annotated in the genome (lipoproteins, multiple-banded antigen like protein, membrane nuclease lipoprotein and variable surface antigens lipoprotein). In addition, a gene encoding glycosyltransferase was also found. This enzyme has been associated with the production of capsule in mycoplasmas and ureaplasma. We then sought to detect the presence of a capsule in this organism. A polysaccharide capsule from 11 to 17 nm of U. diversum was observed trough electron microscopy and using specific dyes. This structure contained arabinose, xylose, mannose, galactose and glucose. In order to understand the inflammatory response against these surface molecules, we evaluated the response of murine macrophages J774 against viable and non-viable U. diversum. As with viable bacteria, non-viable bacteria were capable of promoting a significant inflammatory response by activation of Toll like receptor 2 (TLR2), indicating that surface molecules are important for the activation of inflammatory response. Furthermore, a cascade of genes related to the inflammasome pathway of macrophages was also up-regulated during infection with viable organisms when compared to non-infected cells. In conclusion, U. diversum has a typical ureaplasma genome and metabolism, and

  4. One-dimensional assembling of diiodo[phthalocyaninato(1-)] chromate(III) molecules through neutral I(2) molecules. Alternating ferro- and antiferromagnetic interactions in the metal-radical system.

    Science.gov (United States)

    Janczak, Jan; Idemori, Ynara Marina

    2002-10-07

    Crystals of diiodo[phthalocyaninato(1-)] chromate(III) diiodine, CrPcI(2).I(2), were grown directly in the reaction of chromium powder with 1,2-dicyanobenzene under a stream of iodine at about 250 degrees C. The CrPcI(2).I(2) complex crystallizes in the centrosymmetric space group of the triclinic system with one molecule per unit cell, with the cell dimensions a = 7.851(2) A, b = 8.402(2) A, c = 12.668(3) A, alpha = 80.32(3)(o), beta = 74.06(3)(o), gamma = 82.33(3)(o), and V = 788.7(3) A(3). The X-ray single-crystal analysis shows that each of the centrosymmetric CrPcI(2) molecules is bridged by a neutral I(2) molecule (detected also by Raman spectroscopy) and develops a polymeric one-dimensional structure. The magnetic measurements have been carried out in the temperature range 300-2 K. Temperature dependence of the effective magnetic moment, mu(eff), shows the ferro- and antiferromagnetic interactions in the system of the paramagnetic central Cr(3+) ion and surrounding pi-conjugated radical ligand Pc(1-). The conductivity measurement on a polycrystalline sample exhibits weak temperature dependence (dsigma/dT < 0). The UV-vis spectrum exhibits, besides the B- and Q-bands, one additional band assigned to the electronic transition from a deeper level to the half-occupied HOMO level in the one-electron oxidized phthalocyaninato(1-) radical ligand.

  5. Molecules involved in epithelial-mesenchymal transition and epithelial-stromal interaction in phyllodes tumors: implications for histologic grade and prognosis.

    Science.gov (United States)

    Kwon, Ji Eun; Jung, Woo-Hee; Koo, Ja Seung

    2012-06-01

    The aim of this study was to investigate the expression of molecules associated with epithelial-mesenchymal transition (EMT) and epithelial-stromal interactions (ESI) and to evaluate their roles in phyllodes tumors (PTs). Tissue microarrays (TMAs) were constructed from 207 PT specimens (157 benign, 34 borderline and 16 malignant). The presence of EMT-related markers including N-cadherin, Twist, TGF-beta, HMGA2, S100A4 and Ezrin as well as ESI-related molecules such as SDF1 and CXCR4 among the TMAs was assessed immunohistochemically. Immunohistochemical results were analyzed in terms of clinicopathologic parameters. For higher grade PTs, expressions of Twist (p grade PTs. Further, high expression of Twist in the stromal component was correlated with poorer prognoses.

  6. Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube and in a computer.

    Science.gov (United States)

    Wollman, Adam J M; Miller, Helen; Zhou, Zhaokun; Leake, Mark C

    2015-04-01

    DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA-protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.

  7. Large scale Brownian dynamics of confined suspensions of rigid particles

    Science.gov (United States)

    Sprinkle, Brennan; Balboa Usabiaga, Florencio; Patankar, Neelesh A.; Donev, Aleksandar

    2017-12-01

    We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217-296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its "square" root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose

  8. Large scale Brownian dynamics of confined suspensions of rigid particles.

    Science.gov (United States)

    Sprinkle, Brennan; Balboa Usabiaga, Florencio; Patankar, Neelesh A; Donev, Aleksandar

    2017-12-28

    We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217-296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its "square" root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose

  9. Identification of Small-Molecule Inhibitors of the HuR/RNA Interaction Using a Fluorescence Polarization Screening Assay Followed by NMR Validation.

    Directory of Open Access Journals (Sweden)

    Zhonghua Wang

    Full Text Available The human antigen R (HuR stabilizes many mRNAs of proto-oncogene, transcription factors, cytokines and growth factors by recognizing AU-rich elements (AREs presented in their 3' or 5' untranslated region (UTR. Multiple lines of experimental evidence suggest that this process plays a key role in cancer development. Thus, destabilizing HuR/RNA interaction by small molecules presents an opportunity for cancer treatment/prevention. Here we present an integrated approach to identify inhibitors of HuR/RNA interaction using a combination of fluorescence-based and NMR-based high throughput screening (HTS. The HTS assay with fluorescence polarization readout and Z'-score of 0.8 was used to perform a screen of the NCI diversity set V library in a 384 well plate format. An NMR-based assay with saturation transfer difference (STD detection was used for hits validation. Protein NMR spectroscopy was used to demonstrate that some hit compounds disrupt formation of HuR oligomer, whereas others block RNA binding. Thus, our integrated high throughput approach provides a new avenue for identification of small molecules targeting HuR/RNA interaction.

  10. Interaction Research on the Antiviral Molecule Dufulin Targeting on Southern Rice Black Streaked Dwarf Virus P9-1 Nonstructural Protein

    Directory of Open Access Journals (Sweden)

    Zhenchao Wang

    2015-03-01

    Full Text Available ern rice black streaked dwarf virus (SRBSDV causes severe harm to rice production. Unfortunately, studies on effective antiviral drugs against SRBSDV and interaction mechanism of antiviral molecule targeting on SRBSDV have not been reported. This study found dufulin (DFL, an ideal anti-SRBSDV molecule, and investigated the interactions of DFL targeting on the nonstructural protein P9-1. The biological sequence information and bonding characterization of DFL to four kinds of P9-1 protein were described with fluorescence titration (FT and microscale thermophoresis (MST assays. The sequence analysis indicated that P9-1 had highly-conserved C- and N-terminal amino acid residues and a hypervariable region that differed from 131 aa to 160 aa. Consequently, wild-type (WT-His-P9-1, 23 C-terminal residues truncated (TR-ΔC23-His-P9-1, 6 N-terminal residues truncated (TR-ΔN6-His-P9-1, and Ser138 site-directed (MU-138-His-P9-1 mutant proteins were expressed. The FT and MST assay results indicated that DFL bounded to WT-His-P9-1 with micromole affinity and the 23 C-terminal amino acids were the potential targeting site. This system, which combines a complete sequence analysis, mutant protein expression, and binding action evaluating system, could further advance the understanding of the interaction abilities between antiviral drugs and their targets.

  11. Monitoring Cellular Interactions during T Cell Activation at the Single Molecule Level Using Semiconductor Quantum-Dots

    National Research Council Canada - National Science Library

    Weiss, Shimon; Witte, Owen; Bentolila, Laurent; Pinaud, Fabien; Tsay, James; Radu, Caius; Wang, Lili

    2005-01-01

    ...) were developed. Two high-affinity targeting "velcro-pairs" based on avidin-biotin and fluorescine-antibody interactions were demonstrated and used to specifically target single proteins in membranes of live cells...

  12. Molecule Matters

    Indian Academy of Sciences (India)

    is a very stable and inert molecule due to the formation of a triple bond between the two atoms. Surpris- ingly isoelectronic molecules are quite reactive making dinitrogen very useful and unique. Dinitrogen (N. 2. ) is such an innocuous molecule that you might not think it worthy of special attention. We take this molecule for.

  13. Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore

    Science.gov (United States)

    Wells, Craig C.; Melnikov, Dmitriy V.; Gracheva, Maria E.

    2017-08-01

    We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.

  14. Interaction of multicharged ions with molecules (CO{sub 2}, C{sub 60}) by coincident electron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Moretto-Capelle, P.; Bordenave-Montesquieu, D.; Bordenave-Montesquieu, A. [Universite Paul Sabatier, Toulouse (France). Lab. CAR-IRSAMC

    2001-07-01

    First results for the investigation of electron capture processes in collisions between multicharged ions and molecule targets using electron spectroscopy in coincidence with charged fragments, are presented. It is shown that a much more detailed investigation of the capture reaction can be achieved using molecular instead of heavy atomic targets provided that an analysis of the target dissociation is made. The collisional systems {sup 18}O{sup 8+}+Ar, CO{sub 2} and C{sub 60} have been studied at 80 keV. Non coincident electron spectra as well as first results of double or triple coincidence experiments are discussed. Kinetic energy distributions of the C{sub n}{sup +} fragments (n=1 to 8) produced in multiple capture processes from C{sub 60} target are given. A detailed investigation of the double capture process with CO{sub 2} molecule allows the measurement of kinetic energy release distributions (KERD) which characterize the dissociation of CO{sub 2}{sup 2+} molecular ions; our results are found to be very similar to those measured in double photoionisation experiments. (orig.)

  15. Synthetic strategies for controlling inter- and intramolecular interactions: Applications in single-molecule fluorescence imaging, bioluminescence imaging, and palladium catalysis

    Science.gov (United States)

    Conley, Nicholas R.

    The field of synthetic organic chemistry has reached such maturity that, with sufficient effort and resources, the synthesis of virtually any small molecule which exhibits reasonable stability at room temperature can be realized. While representing a monumental achievement for the field, the ability to exert precise control over molecular structure is just a means to an end, and it is frequently the responsibility of the synthetic chemist to determine which molecules should actually be synthesized. For better or worse, there exists no competitive free market in academia for new molecules, and as a result, the decision of which compounds should be synthesized is seldom driven by the forces of supply and demand; rather, it is guided by the synthetic chemist's interest in an anticipated structure-function relationship or in the properties of a previously unstudied class of molecules. As a consequence, there exists a pervasive need for chemists with synthetic expertise in fields (e.g., molecular imaging) and subdisciplines of chemistry (e.g., physical chemistry) in which the identification of promising synthetic targets dramatically outpaces the synthetic output in that field or subdiscipline, and ample opportunities are available for synthetic chemists who choose to pursue such cross-disciplinary research. This thesis describes synthetic efforts that leverage these opportunities to realize applications in biological imaging and in palladium catalysis. In Part I, the synthesis and characterization of three novel luminophores and their imaging applications are discussed. The first is a molecular beacon that utilizes a fluorophorefluorophore pair which exhibits H-dimer quenching in the closed conformation. This probe offers several advantages over conventional fluorophore-quencher molecular beacons in the detection of oligonucleotides, both in bulk and at the single-molecule level. Secondly, a fluorescent, Cy3-Cy5 covalent heterodimer is reported, which on account of the

  16. Rab interacting molecules 2 and 3 directly interact with the pore-forming CaV1.3 Ca2+ channel subunit and promote its membrane expression.

    OpenAIRE

    Picher, M.; Oprişoreanu, A.; Jung, S.; Michel, K.; Schoch, S.; Moser, T.

    2017-01-01

    Rab interacting molecules (RIMs) are multi-domain proteins that positively regulate the number of Ca2+ channels at the presynaptic active zone (AZ). Several molecular mechanisms have been demonstrated for RIM-binding to components of the presynaptic Ca2+ channel complex, the key signaling element at the AZ. Here, we report an interaction of the C2B domain of RIM2? and RIM3? with the C-terminus of the pore-forming ??subunit of CaV1.3 channels (CaV1.3?1), which mediate stimulus-secretion coupli...

  17. Intermediate scattering function of an anisotropic Brownian circle swimmer.

    Science.gov (United States)

    Kurzthaler, Christina; Franosch, Thomas

    2017-09-27

    Microswimmers exhibit noisy circular motion due to asymmetric propulsion mechanisms, their chiral body shape, or by hydrodynamic couplings in the vicinity of surfaces. Here, we employ the Brownian circle swimmer model and characterize theoretically the dynamics in terms of the directly measurable intermediate scattering function. We derive the associated Fokker-Planck equation for the conditional probabilities and provide an exact solution in terms of generalizations of the Mathieu functions. Different spatiotemporal regimes are identified reflecting the bare translational diffusion at large wavenumbers, the persistent circular motion at intermediate wavenumbers and an enhanced effective diffusion at small wavenumbers. In particular, the circular motion of the particle manifests itself in characteristic oscillations at a plateau of the intermediate scattering function for wavenumbers probing the radius.

  18. Change of particle size distribution during Brownian coagulation

    International Nuclear Information System (INIS)

    Lee, K.W.

    1984-01-01

    Change in particle size distribution due to Brownian coagulation in the continuum regime has been stuied analytically. A simple analytic solution for the size distribution of an initially lognormal distribution is obtained based on the assumption that the size distribution during the coagulation process attains or can, at least, be represented by a time dependent lognormal function. The results are found to be in a form that corrects Smoluchowski's solution for both polydispersity and size-dependent kernel. It is further shown that regardless of whether the initial distribution is narrow or broad, the spread of the distribution is characterized by approaching a fixed value of the geometric standard deviation. This result has been compared with the self-preserving distribution obtained by similarity theory. (Author)

  19. Confined mobility in biomembranes modeled by early stage Brownian motion.

    Science.gov (United States)

    Gmachowski, Lech

    2014-08-01

    An equation of motion, derived from the fractal analysis of the Brownian particle trajectory, makes it possible to calculate the time dependence of the mean square displacement for early times, before the Einstein formula becomes valid. The diffusion coefficient increases with the distance travelled which can be restricted by the geometrical conditions. The corresponding diffusion coefficient cannot increase further to achieve a value characteristic for unrestricted environment. Explicit formula is derived for confined diffusivity related to the unrestricted one as dependent on the maximum particle mean square displacement possible normalized by the square of its mean free path. The model describes the lipid and protein diffusion in tubular membranes with different radii, originally fitted by the modified Saffman-Delbrück equation, and the lateral mobility of synthetic model peptides for which the diffusion coefficient is inversely proportional to the radius of the diffusing object and to the thickness of the membrane. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Brownian rotational relaxation and power absorption in magnetite nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Goya, G.F. [Institute of Nanoscience of Aragon (INA), University of Zaragoza, 50009 Zaragoza (Spain)]. E-mail: goya@unizar.es; Fernandez-Pacheco, R. [Institute of Nanoscience of Aragon (INA), University of Zaragoza, 50009 Zaragoza (Spain); Arruebo, M. [Institute of Nanoscience of Aragon (INA), University of Zaragoza, 50009 Zaragoza (Spain); Cassinelli, N. [Electronics Division, Bauer and Associates, Buenos Aires (Argentina); Facultad de Ingenieria, UNLP (Argentina); Ibarra, M.R. [Institute of Nanoscience of Aragon (INA), University of Zaragoza, 50009 Zaragoza (Spain)

    2007-09-15

    We present a study of the power absorption efficiency in several magnetite-based colloids, to asses their potential as magnetic inductive hyperthermia (MIH) agents. Relaxation times {tau} were measured through the imaginary susceptibility component {chi}{sup '}'(T), and analyzed within Debye's theory of dipolar fluid. The results indicated Brownian rotational relaxation and allowed to calculate the hydrodynamic radius close to the values obtained from photon correlation. The study of the colloid performances as power absorbers showed no detectable increase of temperature for dextran-coated Fe{sub 3}O{sub 4} nanoparticles, whereas a second Fe{sub 3}O{sub 4}-based dispersion of similar concentration could be heated up to 12K after 30min under similar experimental conditions. The different power absorption efficiencies are discussed in terms of the magnetic structure of the nanoparticles.

  1. Large Scale Brownian Dynamics of Confined Suspensions of Rigid Particles

    Science.gov (United States)

    Donev, Aleksandar; Sprinkle, Brennan; Balboa, Florencio; Patankar, Neelesh

    2017-11-01

    We introduce new numerical methods for simulating the dynamics of passive and active Brownian colloidal suspensions of particles of arbitrary shape sedimented near a bottom wall. The methods also apply for periodic (bulk) suspensions. Our methods scale linearly in the number of particles, and enable previously unprecedented simulations of tens to hundreds of thousands of particles. We demonstrate the accuracy and efficiency of our methods on a suspension of boomerang-shaped colloids. We also model recent experiments on active dynamics of uniform suspensions of spherical microrollers. This work was supported in part by the National Science Foundation under award DMS-1418706, and by the U.S. Department of Energy under award DE-SC0008271.

  2. Optimal dividends in the Brownian motion risk model with interest

    Science.gov (United States)

    Fang, Ying; Wu, Rong

    2009-07-01

    In this paper, we consider a Brownian motion risk model, and in addition, the surplus earns investment income at a constant force of interest. The objective is to find a dividend policy so as to maximize the expected discounted value of dividend payments. It is well known that optimality is achieved by using a barrier strategy for unrestricted dividend rate. However, ultimate ruin of the company is certain if a barrier strategy is applied. In many circumstances this is not desirable. This consideration leads us to impose a restriction on the dividend stream. We assume that dividends are paid to the shareholders according to admissible strategies whose dividend rate is bounded by a constant. Under this additional constraint, we show that the optimal dividend strategy is formed by a threshold strategy.

  3. BROWNIAN HEAT TRANSFER ENHANCEMENT IN THE TURBULENT REGIME

    Directory of Open Access Journals (Sweden)

    Suresh Chandrasekhar

    2016-08-01

    Full Text Available The paper presents convection heat transfer of a turbulent flow Al2O3/water nanofluid in a circular duct. The duct is a under constant and uniform heat flux. The paper computationally investigates the system’s thermal behavior in a wide range of Reynolds number and also volume concentration up to 6%. To obtain the nanofluid thermophysical properties, the Hamilton-Crosser model along with the Brownian motion effect are utilized. Then the thermal performance of the system with the nanofluid is compared to the conventional systems which use water as the working fluid. The results indicate that the use of nanofluid of 6% improves the heat transfer rate up to 36.8% with respect to pure water. Therefore, using the Al2O3/water nanofluid instead of water can be a great choice when better heat transfer is needed.

  4. Semicircular canals circumvent Brownian Motion overload of mechanoreceptor hair cells

    DEFF Research Database (Denmark)

    Muller, Mees; Heeck, Kier; Elemans, Coen P H

    2016-01-01

    Vertebrate semicircular canals (SCC) first appeared in the vertebrates (i.e. ancestral fish) over 600 million years ago. In SCC the principal mechanoreceptors are hair cells, which as compared to cochlear hair cells are distinctly longer (70 vs. 7 μm), 10 times more compliant to bending (44 vs. 500...... nN/m), and have a 100-fold higher tip displacement threshold (hair cells where the bundle is approximated as a stiff, cylindrical elastic rod subject to friction and thermal agitation. Our models suggest that the above...... differences aid SCC hair cells in circumventing the masking effects of Brownian motion noise of about 70 nm, and thereby permit transduction of very low frequency (

  5. Modeling collective emotions: a stochastic approach based on Brownian agents

    International Nuclear Information System (INIS)

    Schweitzer, F.

    2010-01-01

    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)

  6. Monitoring autocorrelated process: A geometric Brownian motion process approach

    Science.gov (United States)

    Li, Lee Siaw; Djauhari, Maman A.

    2013-09-01

    Autocorrelated process control is common in today's modern industrial process control practice. The current practice of autocorrelated process control is to eliminate the autocorrelation by using an appropriate model such as Box-Jenkins models or other models and then to conduct process control operation based on the residuals. In this paper we show that many time series are governed by a geometric Brownian motion (GBM) process. Therefore, in this case, by using the properties of a GBM process, we only need an appropriate transformation and model the transformed data to come up with the condition needs in traditional process control. An industrial example of cocoa powder production process in a Malaysian company will be presented and discussed to illustrate the advantages of the GBM approach.

  7. On the first-passage time of integrated Brownian motion

    Directory of Open Access Journals (Sweden)

    Christian H. Hesse

    2005-01-01

    Full Text Available Let (Bt;t≥0 be a Brownian motion process starting from B0=ν and define Xν(t=∫0tBsds. For a≥0, set τa,ν:=inf{t:Xν(t=a} (with inf φ=∞. We study the conditional moments of τa,ν given τa,ν<∞. Using martingale methods, stopping-time arguments, as well as the method of dominant balance, we obtain, in particular, an asymptotic expansion for the conditional mean E(τa,ν|τa,ν<∞ as ν→∞. Through a series of simulations, it is shown that a truncation of this expansion after the first few terms provides an accurate approximation to the unknown true conditional mean even for small ν.

  8. Filamin A Modulates Store-Operated Ca2+ Entry by Regulating STIM1 (Stromal Interaction Molecule 1)-Orai1 Association in Human Platelets.

    Science.gov (United States)

    Lopez, Jose J; Albarrán, Letizia; Jardín, Isaac; Sanchez-Collado, Jose; Redondo, Pedro C; Bermejo, Nuria; Bobe, Regis; Smani, Tarik; Rosado, Juan A

    2018-02-01

    Here, we provide evidence for the role of FLNA (filamin A) in the modulation of store-operated calcium entry (SOCE). SOCE is a major mechanism for calcium influx controlled by the intracellular Ca 2+ stores. On store depletion, the endoplasmic reticulum calcium sensor STIM1 (stromal interaction molecule 1) redistributes into puncta at endoplasmic reticulum/plasma membrane junctions, a process supported by the cytoskeleton, where it interacts with the calcium channels; however, the mechanism for fine-tuning SOCE is not completely understood. Our results demonstrate that STIM1 interacts with FLNA on calcium store depletion in human platelets. The interaction is dependent on the phosphorylation of FLNA at Ser 2152 by the cAMP-dependent protein kinase. Impairment of FLNA phosphorylation and knockdown of FLNA expression using siRNA increased SOCE in platelets. Similarly, SOCE was significantly greater in FLNA-deficient melanoma M2 cells than in the FLNA-expressing M2 subclone A7. Expression of FLNA in M2 cells attenuated SOCE, an effect prevented when the cells were transfected with the nonphosphorylatable FLNA S2152A mutant. Transfection of M2 cells with the STIM1(K684,685E) mutant reduced the STIM1-FLNA interaction. In platelets, attenuation of FLNA expression using siRNA resulted in enhanced association of STIM1 with the cytoskeleton, greater STIM1-Orai1 interaction, and SOCE. Introduction of an anti-FLNA (2597-2647) antibody attenuated the STIM1-FLNA interaction and enhanced thrombin-induced platelet aggregation. Our results indicate that FLNA modulates SOCE and then the correct platelet function, by fine-tuning the distribution of STIM1 in the cytoskeleton and the interaction with Orai1 channels. © 2017 American Heart Association, Inc.

  9. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  10. Enhancing the blocking temperature in single-molecule magnets by incorporating 3d-5d exchange interactions

    DEFF Research Database (Denmark)

    Pedersen, Kasper Søndergaard; Schau-Magnussen, Magnus; Bendix, Jesper

    2010-01-01

    We report the first single-molecule magnet (SMM) to incorporate the [Os(CN)(6)](3-) moiety. The compound (1) has a trimeric, cyanide-bridged Mn(III)-Os(III)-Mn(III) skeleton in which Mn(III) designates a [Mn(5-Brsalen)(MeOH)](+) unit (5-Brsalen=N,N'-ethylenebis(5-bromosalicylideneiminato)). X......-ray crystallographic experiments reveal that 1 is isostructural with the Mn(III)-Fe(III)-Mn(III) analogue (2). Both compounds exhibit a frequency-dependent out-of-phase ¿''(T) alternating current (ac) susceptibility signal that is suggestive of SMM behaviour. From the Arrhenius expression, the effective barrier for 1...... for the design of a new generation of SMMs with enhanced SMM properties....

  11. A Stability Result for Stochastic Differential Equations Driven by Fractional Brownian Motions

    Directory of Open Access Journals (Sweden)

    Bruno Saussereau

    2012-01-01

    Full Text Available We study the stability of the solutions of stochastic differential equations driven by fractional Brownian motions with Hurst parameter greater than half. We prove that when the initial conditions, the drift, and the diffusion coefficients as well as the fractional Brownian motions converge in a suitable sense, then the sequence of the solutions of the corresponding equations converge in Hölder norm to the solution of a stochastic differential equation. The limit equation is driven by the limit fractional Brownian motion and its coefficients are the limits of the sequence of the coefficients.

  12. ESR study on the interaction between carbon blacks and oxygen molecules; ESR ho ni yoru carbon black to sanso bunshi tono sogo sayo no kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Okazaki, M.; Toriyama, K.; Konishi, Y. [National Industrial Research Institute of Nagoya, Nagoya (Japan)

    2000-02-24

    Interaction between carbon blacks and oxygen molecules has been studied by means of electron spin resonance (ESR) spectroscopy. The ESR spectra of the carbon blacks appears at the g-value of free spin, which are contributed by both isolated electrons and conduction electrons. Upon introducing oxygen to the system the ESR linewidth was broadened in proportion to the partial pressure of oxygen. In case of lampblack (LB 101, Degussa) the interaction was not so strong that it took a tong time at 77K for the linewidth to reach the maxmum value. In case of gassblack (P 140 V, Degussa), on the other hand, the oxygen was easily adsorbed at 298K and the linewidth at 77K became its maximum immediately after cooling. The number of unpaired electrons decreased when the system was kept at 298 K and the decrease was prominent for the local spins. These phenomena have been explained with a simple band model for the electron. (author)

  13. A fiber-modified adenoviral vector interacts with immunoevasion molecules of the B7 family at the surface of murine leukemia cells derived from dormant tumors

    Directory of Open Access Journals (Sweden)

    Rogée Sophie

    2011-08-01

    Full Text Available Abstract Tumor cells can escape the immune system by overexpressing molecules of the B7 family, e.g. B7-H1 (PD-L1 or CD86, which suppresses the anti-tumor T-cell responses through binding to the PD-1 receptor, and similarly for B7.1 (CD80, through binding to CTLA-4. Moreover, direct interactions between B7-H1 and B7.1 molecules are also likely to participate in the immunoevasion mechanism. In this study, we used a mouse model of tumor dormancy, DA1-3b leukemia cells. We previously showed that a minor population of DA1-3b cells persists in equilibrium with the immune system for long periods of time, and that the levels of surface expression of B7-H1 and B7.1 molecules correlates with the dormancy time. We found that leukemia cells DA1-3b/d365 cells, which derived from long-term dormant tumors and overexpressed B7-H1 and B7.1 molecules, were highly permissive to Ad5FB4, a human adenovirus serotype 5 (Ad5 vector pseudotyped with chimeric human-bovine fibers. Both B7-H1 and B7.1 were required for Ad5FB4-cell binding and entry, since (i siRNA silencing of one or the other B7 gene transcript resulted in a net decrease in the cell binding and Ad5FB4-mediated transduction of DA1-3b/d365; and (ii plasmid-directed expression of B7.1 and B7-H1 proteins conferred to Ad5FB4-refractory human cells a full permissiveness to this vector. Binding data and flow cytometry analysis suggested that B7.1 and B7-H1 molecules played different roles in Ad5FB4-mediated transduction of DA1-3b/d365, with B7.1 involved in cell attachment of Ad5FB4, and B7-H1 in Ad5FB4 internalization. BRET analysis showed that B7.1 and B7-H1 formed heterodimeric complexes at the cell surface, and that Ad5FB4 penton, the viral capsomere carrying the fiber projection, could negatively interfere with the formation of B7.1/B7-H1 heterodimers, or modify their conformation. As interactors of B7-H1/B7.1 molecules, Ad5FB4 particles and/or their penton capsomeres represent potential therapeutic agents

  14. Effect of H-bonding interactions of water molecules in the self assembly of supramolecular architecture-joint experimental and computational studies

    Science.gov (United States)

    Jassal, Amanpreet Kaur; Kaur, Rajwinder; Islam, Nasarul; Anu; Mudsainiyan, Rahul Kumar

    2017-08-01

    A new {[Cu(4,4‧-BP)2.(H2O)4].2,6-NDC.3(H2O)} complex has been synthesized by refluxing Cu(NO3)2, 2,6-NDC and 4,4‧-BP (1:1:1 ratio) (2,6-NDC = 2,6-Naphthalene Dicarboxylic acid, 4,4‧-BP = 4,4'-bipyridine) in methanol/ammonia mixture and characterized by various spectroscopic techniques. The geometry around Cu2+ ion is typical octahedral in cationic complex, while the deprotonated 2,6-NDC act as a charge balancing counter anionic part. Water molecules (lattice and coordinated) also play important role in the self-assembly by forming Hsbnd bonded supramolecular architecture involving strong inter/intramolecular secondary interactions. The luminescence property and thermogravimetric analyses were also investigated. Both the intermolecular interactions of molecular and crystal structures of this complex were compared and discussed using Hirshfeld surface analysis and 2D-fingerprint plots. Hirshfeld surface analysis indicates that H⋯H, O⋯H and π···π contacts can account for 40.4, 19.3 and 7.7% respectively of the total Hirshfeld surface area. The DFT calculation at the CAM-B3LYP level of theory revealed the existence of three hydrogens binds in the complex. These hydrogen bonds exist between the oxygen atom of ligand and the hydrogen of coordinated water molecules.

  15. Theoretical predictions of diffusion from Brownian motion in superstrong polymers

    International Nuclear Information System (INIS)

    Dowell, F.

    1991-01-01

    This paper presents a summary of unique highly nonlinear static and dynamic theories for chain molecules (actually, for almost any kind of organic molecule), including the first superstrong polymers. These theories have been used to predict and explain (1) the physical self-assembly (self-ordering) of specific kinds of molecules into liquid crystalline (LC) phases (i.e., partially ordered phases) and (2) the diffusion of these molecules in various LC phases and the isotropic (I) liquid phase

  16. Drag force and transport property of a small cylinder in free molecule flow: A gas-kinetic theory analysis.

    Science.gov (United States)

    Liu, Changran; Li, Zhigang; Wang, Hai

    2016-08-01

    Analytical expressions are derived for aerodynamic drag force on small cylinders in the free molecule flow using the gas-kinetic theory. The derivation considers the effect of intermolecular interactions between the cylinder and gas media. Two limiting collision models, specular and diffuse scattering, are investigated in two limiting cylinder orientations with respect to the drift velocity. The earlier solution of Dahneke [B. E. Dahneke, J. Aerosol Sci. 4, 147 (1973)10.1016/0021-8502(73)90066-9] is shown to be a special case of the current expressions in the rigid-body limit of collision. Drag force expressions are obtained for cylinders that undergo Brownian rotation and for those that align with the drift velocity. The validity of the theoretical expressions is tested against experimental mobility data available for carbon nanotubes.

  17. Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods

    Science.gov (United States)

    Tao, Yu-Guo; den Otter, W. K.; Padding, J. T.; Dhont, J. K. G.; Briels, W. J.

    2005-06-01

    Recently a microscopic theory for the dynamics of suspensions of long thin rigid rods was presented, confirming and expanding the well-known theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here this theory is put to the test by comparing it against computer simulations. A Brownian dynamics simulation program was developed to follow the dynamics of the rods, with a length over a diameter ratio of 60, on the Smoluchowski time scale. The model accounts for excluded volume interactions between rods, but neglects hydrodynamic interactions. The self-rotational diffusion coefficients Dr(φ) of the rods were calculated by standard methods and by a new, more efficient method based on calculating average restoring torques. Collective decay of orientational order was calculated by means of equilibrium and nonequilibrium simulations. Our results show that, for the currently accessible volume fractions, the decay times in both cases are virtually identical. Moreover, the observed decay of diffusion coefficients with volume fraction is much quicker than predicted by the theory, which is attributed to an oversimplification of dynamic correlations in the theory.

  18. Spontaneous Detachment of Colloids from Primary Energy Minima by Brownian Diffusion.

    Directory of Open Access Journals (Sweden)

    Zhan Wang

    Full Text Available The Derjaguin-Landau-Verwey-Overbeek (DLVO interaction energy profile has been frequently used to interpret the mechanisms controlling colloid attachment/detachment and aggregation/disaggregation behavior. This study highlighted a type of energy profile that is characterized by a shallow primary energy well (i.e., comparable to the average kinetic energy of a colloid at a small separation distance and a monotonic decrease of interaction energy with separation distance beyond the primary energy well. This energy profile is present due to variations of height, curvature, and density of discrete physical heterogeneities on collector surfaces. The energy profile indicates that colloids can be spontaneously detached from the shallow primary energy well by Brownian diffusion. The spontaneous detachment from primary minima was unambiguously confirmed by conducting laboratory column transport experiments involving flow interruptions for two model colloids (polystyrene latex microspheres and engineered nanoparticles (fullerene C60 aggregates. Whereas the spontaneous detachment has been frequently attributed to attachment in secondary minima in the literature, our study indicates that the detached colloids could be initially attached at primary minima. Our study further suggests that the spontaneous disaggregation from primary minima is more significant than spontaneous detachment because the primary minimum depth between colloid themselves is lower than that between a colloid and a collector surface.

  19. Spontaneous Detachment of Colloids from Primary Energy Minima by Brownian Diffusion.

    Science.gov (United States)

    Wang, Zhan; Jin, Yan; Shen, Chongyang; Li, Tiantian; Huang, Yuanfang; Li, Baoguo

    2016-01-01

    The Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energy profile has been frequently used to interpret the mechanisms controlling colloid attachment/detachment and aggregation/disaggregation behavior. This study highlighted a type of energy profile that is characterized by a shallow primary energy well (i.e., comparable to the average kinetic energy of a colloid) at a small separation distance and a monotonic decrease of interaction energy with separation distance beyond the primary energy well. This energy profile is present due to variations of height, curvature, and density of discrete physical heterogeneities on collector surfaces. The energy profile indicates that colloids can be spontaneously detached from the shallow primary energy well by Brownian diffusion. The spontaneous detachment from primary minima was unambiguously confirmed by conducting laboratory column transport experiments involving flow interruptions for two model colloids (polystyrene latex microspheres) and engineered nanoparticles (fullerene C60 aggregates). Whereas the spontaneous detachment has been frequently attributed to attachment in secondary minima in the literature, our study indicates that the detached colloids could be initially attached at primary minima. Our study further suggests that the spontaneous disaggregation from primary minima is more significant than spontaneous detachment because the primary minimum depth between colloid themselves is lower than that between a colloid and a collector surface.

  20. [Aerodynamic focusing of particles and heavy molecules

    International Nuclear Information System (INIS)

    de la Mora, J.F.

    1990-01-01

    By accelerating a gas containing suspended particles or large molecules through a converging nozzle, the suspended species may be focused and therefore used to write fine lines on a surface. Our objective was to study the limits on how narrow this focal region could be as a function of particle size. We find that, for monodisperse particles with masses m p some 3.6 x 10 5 times larger than the molecular mass m of the carrier gas (diameters above some 100 angstrom), there is no fundamental obstacle to directly write submicron features. However, this conclusion has been verified experimentally only with particles larger than 0.1 μm. Experimental, theoretical and numerical studies on the defocusing role of Brownian motion for very small particles or heavy molecules have shown that high resolution (purely aerodynamic) focusing is impossible with volatile molecules whose masses are typically smaller than 1000 Dalton. For these, the minimal focal diameter after optimization appears to be 5√(m/m p ) times the nozzle diameter d n . But combinations of focused lasers and aerodynamic focusing appear as promising for direct writing with molecular precursors. Theoretical and numerical schemes capable of predicting the evolution of the focusing beam, including Brownian motion effects, have been developed, although further numerical work would be desirable. 11 refs

  1. Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations.

    Science.gov (United States)

    Sun, Dong-Ru; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2017-03-01

    Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation and binding free energy studies were performed to investigate the biochemistry behaviors of two class inhibitors binding to matriptase. The binding free energies predicted by MM/GBSA methods are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. The key residues responsible for achieving strong binding have been identified by the MM/GBSA free energy decomposition analysis. Especially, Trp215 and Phe99 had an important impact on active site architecture and ligand binding. The results clearly identify the two class inhibitors exist different binding modes. Through summarizing the two different modes, we have mastered some important and favorable interaction patterns between matriptase and inhibitors. Our findings would be helpful for understanding the interaction mechanism between the inhibitor and matriptase and afford important guidance for the rational design of potent matriptase inhibitors.

  2. Probing Interactions of N-Donor Molecules with Open Metal Sites within Paramagnetic Cr-MIL-101: A Solid-State NMR Spectroscopic and Density Functional Theory Study.

    Science.gov (United States)

    Wittmann, Thomas; Mondal, Arobendo; Tschense, Carsten B L; Wittmann, Johannes J; Klimm, Ottokar; Siegel, Renée; Corzilius, Björn; Weber, Birgit; Kaupp, Martin; Senker, Juergen

    2018-02-14

    Understanding host-guest interactions is one of the key requirements for adjusting properties in metal-organic frameworks (MOFs). In particular, systems with coordinatively unsaturated Lewis acidic metal sites feature highly selective adsorption processes. This is attributed to strong interactions with Lewis basic guest molecules. Here we show that a combination of 13 C MAS NMR spectroscopy with state-of-the-art density functional theory (DFT) calculations allows one to unravel the interactions of water, 2-aminopyridine, 3-aminopyridine, and diethylamine with the open metal sites in Cr-MIL-101. The 13 C MAS NMR spectra, obtained with ultrafast magic-angle spinning, are well resolved, with resonances distributed over 1000 ppm. They present a clear signature for each guest at the open metal sites. Based on competition experiments this leads to the following binding preference: water open metal sites, the NMR data offer additional information about the guest and framework dynamics. We expect that our strategy has the potential for probing the binding situation of adsorbate mixtures at the open metal sites of MOFs in general and thus accesses the microscopic interaction mechanisms for this important material class, which is essential for deriving structure-property relationships.

  3. Landau-Zener tunneling in the presence of weak intermolecular interactions in a crystal of Mn4 single-molecule magnets

    Science.gov (United States)

    Wernsdorfer, W.; Bhaduri, S.; Vinslava, A.; Christou, G.

    2005-12-01

    A Mn4 single-molecule magnet (SMM), with a well-isolated spin ground state of S=9/2 , is used as a model system to study Landau-Zener (LZ) tunneling in the presence of weak intermolecular dipolar and exchange interactions. The anisotropy constants D and B are measured with minor hysteresis loops. A transverse field is used to tune the tunnel splitting over a large range. Using the LZ and inverse LZ method, it is shown that these interactions play an important role in the tunnel rates. Three regions are identified: (i) at small transverse fields, tunneling is dominated by single tunnel transitions, (ii) at intermediate transverse fields, the measured tunnel rates are governed by reshuffling of internal fields, and (iii) at larger transverse fields, the magnetization reversal starts to be influenced by the direct relaxation process, and many-body tunnel events may occur. The hole digging method is used to study the next-nearest-neighbor interactions. At small external fields, it is shown that magnetic ordering occurs which does not quench tunneling. An applied transverse field can increase the ordering rate. Spin-spin cross-relaxations, mediated by dipolar and weak exchange interactions, are proposed to explain additional quantum steps.

  4. Molecule nanoweaver

    Science.gov (United States)

    Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  5. Second order limit laws for occupation times of the fractional Brownian motion

    OpenAIRE

    Xu, Fangjun

    2013-01-01

    We prove second order limit laws for (additive) functionals of the $d$-dimensional fractional Brownian motion with Hurst index $H=\\frac{1}{d}$, using the method of moments, extending the Kallianpur-Robbins law.

  6. Self-Intersection Local Times of Generalized Mixed Fractional Brownian Motion as White Noise Distributions

    International Nuclear Information System (INIS)

    Suryawan, Herry P.; Gunarso, Boby

    2017-01-01

    The generalized mixed fractional Brownian motion is defined by taking linear combinations of a finite number of independent fractional Brownian motions with different Hurst parameters. It is a Gaussian process with stationary increments, posseses self-similarity property, and, in general, is neither a Markov process nor a martingale. In this paper we study the generalized mixed fractional Brownian motion within white noise analysis framework. As a main result, we prove that for any spatial dimension and for arbitrary Hurst parameter the self-intersection local times of the generalized mixed fractional Brownian motions, after a suitable renormalization, are well-defined as Hida white noise distributions. The chaos expansions of the self-intersection local times in the terms of Wick powers of white noises are also presented. (paper)

  7. Self-Intersection Local Times of Generalized Mixed Fractional Brownian Motion as White Noise Distributions

    Science.gov (United States)

    Suryawan, Herry P.; Gunarso, Boby

    2017-06-01

    The generalized mixed fractional Brownian motion is defined by taking linear combinations of a finite number of independent fractional Brownian motions with different Hurst parameters. It is a Gaussian process with stationary increments, posseses self-similarity property, and, in general, is neither a Markov process nor a martingale. In this paper we study the generalized mixed fractional Brownian motion within white noise analysis framework. As a main result, we prove that for any spatial dimension and for arbitrary Hurst parameter the self-intersection local times of the generalized mixed fractional Brownian motions, after a suitable renormalization, are well-defined as Hida white noise distributions. The chaos expansions of the self-intersection local times in the terms of Wick powers of white noises are also presented.

  8. Cold Rydberg molecules

    Science.gov (United States)

    Raithel, Georg; Zhao, Jianming

    2017-04-01

    Cold atomic systems have opened new frontiers at the interface of atomic and molecular physics. These include research on novel types of Rydberg molecules. Three types of molecules will be reviewed. Long-range, homonuclear Rydberg molecules, first predicted in [1] and observed in [2], are formed via low-energy electron scattering of the Rydberg electron from a ground-state atom within the Rydberg atom's volume. The binding mostly arises from S- and P-wave triplet scattering. We use a Fermi model that includes S-wave and P-wave singlet and triplet scattering, the fine structure coupling of the Rydberg atom and the hyperfine structure coupling of the 5S1/2 atom (in rubidium [3]). The hyperfine structure gives rise to mixed singlet-triplet potentials for both low-L and high-L Rydberg molecules [3]. A classification into Hund's cases [3, 4, 5] will be discussed. The talk further includes results on adiabatic potentials and adiabatic states of Rydberg-Rydberg molecules in Rb and Cs. These molecules, which have even larger bonding length than Rydberg-ground molecules, are formed via electrostatic multipole interactions. The leading interaction term of neutral Rydberg-Rydberg molecules is between two dipoles, while for ionic Rydberg molecules it is between a dipole and a monopole. NSF (PHY-1506093), NNSF of China (61475123).

  9. All mammalian Hedgehog proteins interact with cell adhesion molecule, down-regulated by oncogenes (CDO) and brother of CDO (BOC) in a conserved manner.

    Science.gov (United States)

    Kavran, Jennifer M; Ward, Matthew D; Oladosu, Oyindamola O; Mulepati, Sabin; Leahy, Daniel J

    2010-08-06

    Hedgehog (Hh) signaling proteins stimulate cell proliferation, differentiation, and tissue patterning at multiple points in animal development. A single Hh homolog is present in Drosophila, but three Hh homologs, Sonic Hh, Indian Hh, and Desert Hh, are present in mammals. Distribution, movement, and reception of Hh signals are tightly regulated, and abnormal Hh signaling is associated with developmental defects and cancer. In addition to the integral membrane proteins Patched and Smoothened, members of the Drosophila Ihog family of adhesion-like molecules have recently been shown to bind Hh proteins with micromolar affinity and positively regulate Hh signaling. Cell adhesion molecule-related, down-regulated by oncogenes (CDO) and Brother of CDO (BOC) are the closest mammalian relatives of Drosophila Ihog, and CDO binds Sonic Hh with micromolar affinity and positively regulates Hh signaling. Despite these similarities, structural and biochemical studies have shown that Ihog and CDO utilize nonorthologous domains and completely different binding modes to interact with cognate Hh proteins. We report here biochemical and x-ray structural studies of Sonic, Indian, and Desert Hh proteins both alone and complexed with active domains of CDO and BOC. These results show that all mammalian Hh proteins bind CDO and BOC in the same manner. We also show that interactions between Hh proteins and CDO are weakened at low pH. Formation of Hh-mediated Hh oligomers is thought to be an important feature of normal Hh signaling, but no conserved self-interaction between Hh proteins is apparent from inspection of 14 independent Hh-containing crystal lattices.

  10. On the distribution of estimators of diffusion constants for Brownian motion

    International Nuclear Information System (INIS)

    Boyer, Denis; Dean, David S

    2011-01-01

    We discuss the distribution of various estimators for extracting the diffusion constant of single Brownian trajectories obtained by fitting the squared displacement of the trajectory. The analysis of the problem can be framed in terms of quadratic functionals of Brownian motion that correspond to the Euclidean path integral for simple Harmonic oscillators with time dependent frequencies. Explicit analytical results are given for the distribution of the diffusion constant estimator in a number of cases and our results are confirmed by numerical simulations.

  11. The probability of an encounter of two Brownian particles before escape

    International Nuclear Information System (INIS)

    Holcman, D; Kupka, I

    2009-01-01

    We study the probability of meeting of two Brownian particles before one of them exits a finite interval. We obtain an explicit expression for the probability as a function of the initial distance between 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.

  12. Asian Option Pricing with Monotonous Transaction Costs under Fractional Brownian Motion

    Directory of Open Access Journals (Sweden)

    Di Pan

    2013-01-01

    Full Text Available Geometric-average Asian option pricing model with monotonous transaction cost rate under fractional Brownian motion was established. The method of partial differential equations was used to solve this model and the analytical expressions of the Asian option value were obtained. The numerical experiments show that Hurst exponent of the fractional Brownian motion and transaction cost rate have a significant impact on the option value.

  13. Integrated fractional white noise as an alternative to multifractional Brownian motion

    OpenAIRE

    Sly, Allan

    2007-01-01

    Multifractional Brownian motion is a Gaussian process which has changing scaling properties generated by varying the local Hölder exponent. We show that multifractional Brownian motion is very sensitive to changes in the selected Hölder exponent and has extreme changes in magnitude. We suggest an alternative stochastic process, called integrated fractional white noise, which retains the important local properties but avoids the undesirable oscillations in magnitude. We also show h...

  14. Weak solutions to stochastic differential equations driven by fractional Brownian motion

    Czech Academy of Sciences Publication Activity Database

    Šnupárková, Jana

    2009-01-01

    Roč. 59, č. 4 (2009), s. 879-907 ISSN 0011-4642 R&D Projects: GA ČR GA201/07/0237 Institutional research plan: CEZ:AV0Z10750506 Keywords : fractional Brownian motion * weak solutions Subject RIV: BA - General Mathematics Impact factor: 0.306, year: 2009 http://library.utia.cas.cz/separaty/2009/SI/snuparkova-weak solutions to stochastic differential equations driven by fractional brownian motion.pdf

  15. Attractive and repulsive interactions among methanol molecules in supercritical state investigated by Raman spectroscopy and perturbed hard-sphere theory.

    Science.gov (United States)

    Saitow, Ken-ichi; Sasaki, Jungo

    2005-03-08

    , inhomogeneous width, and local density. The density fluctuation in the vicinity of a vibrating molecule is compared to the fluctuation of bulk density, which is obtained from the thermodynamic calculation.

  16. Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy.

    Science.gov (United States)

    Banerjee, S; Rakshit, T; Sett, S; Mukhopadhyay, R

    2015-10-22

    One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.

  17. Thermophoretic forces on DNA measured with a single-molecule spring balance

    DEFF Research Database (Denmark)

    Pedersen, Jonas Nyvold; Lüscher, Christopher James; Marie, Rodolphe

    2014-01-01

    of the thermophoretic force in a static configuration finds forces up to 130 fN. This is eleven times stronger than the force experienced by the same molecule in the same thermal gradient in bulk, where the molecule shields itself. Our stronger forces stretch the middle of the molecule up to 80% of its contour length......We stretch a single DNA molecule with thermophoretic forces and measure these forces with a spring balance: the DNA molecule itself. It is an entropic spring which we calibrate, using as a benchmark its Brownian motion in the nanochannel that contains and prestretches it. This direct measurement...

  18. Molecular evolution and functional divergence of the Ca(2+ sensor protein in store-operated Ca(2+ entry: stromal interaction molecule.

    Directory of Open Access Journals (Sweden)

    Xinjiang Cai

    2007-07-01

    Full Text Available Receptor-mediated Ca(2+ signaling in many non-excitable cells initially induces Ca(2+ release from intracellular Ca(2+ stores, followed by Ca(2+ influx across the plasma membrane. Recent findings have suggested that stromal interaction molecules (STIMs function as the Ca(2+ sensor to detect changes of Ca(2+ content in the intracellular Ca(2+ stores. Human STIMs and invertebrate STIM share several functionally important protein domains, but diverge significantly in the C-terminus. To better understand the evolutionary significance of STIM activity, phylogenetic analysis of the STIM protein family was conducted after extensive database searching. Results from phylogeny and sequence analysis revealed early adaptation of the C-terminal divergent domains in Urochordata, before the expansion of STIMs in Vertebrata. STIMs were subsequently subjected to one round of gene duplication as early as in the Euteleostomi lineage in vertebrates, with a second round of fish-specific gene duplication. After duplication, STIM-1 and STIM-2 molecules appeared to have undergone purifying selection indicating strong evolutionary constraints within each group. Furthermore, sequence analysis of the EF-hand Ca(2+ binding domain and the SAM domain, together with functional divergence studies, identified critical regions/residues likely underlying functional changes, and provided evidence for the hypothesis that STIM-1 and STIM-2 might have developed distinct functional properties after duplication.

  19. Lorentz-like force emerging from kinematic interactions between electrons and nuclei in molecules: A quantum mechanical origin of symmetry breaking that can trigger molecular chirality

    Science.gov (United States)

    Takatsuka, Kazuo

    2017-02-01

    The Longuet-Higgins (Berry) phase arising from nonadiabatic dynamics and the Aharonov-Bohm phase associated with the dynamics of a charged particle in the electromagnetic vector potential are well known to be individually a manifestation of a class of the so-called geometrical phase. We herein discuss another similarity between the force working on a charged particle moving in a magnetic field, the Lorentz force, and a force working on nuclei while passing across a region where they have a strong quantum mechanical kinematic (nonadiabatic) coupling with electrons in a molecule. This kinematic force is indeed akin to the Lorentz force in that its magnitude is proportional to the velocity of the relevant nuclei and works in the direction perpendicular to its translational motion. Therefore this Lorentz-like nonadiabatic force is realized only in space of more or equal to three dimensions, thereby highlighting a truly multi-dimensional effect of nonadiabatic interaction. We investigate its physical significance qualitatively in the context of breaking of molecular spatial symmetry, which is not seen otherwise without this force. This particular symmetry breaking is demonstrated in application to a coplanar collision between a planar molecule and an atom sharing the same plane. We show that the atom is guided by this force to the direction out from the plane, resulting in a configuration that distinguishes one side of the mirror plane from the other. This can serve as a trigger for the dynamics towards molecular chirality.

  20. Negative mobility of a Brownian particle: Strong damping regime

    Science.gov (United States)

    Słapik, A.; Łuczka, J.; Spiechowicz, J.

    2018-02-01

    We study impact of inertia on directed transport of a Brownian particle under non-equilibrium conditions: the particle moves in a one-dimensional periodic and symmetric potential, is driven by both an unbiased time-periodic force and a constant force, and is coupled to a thermostat of temperature T. Within selected parameter regimes this system exhibits negative mobility, which means that the particle moves in the direction opposite to the direction of the constant force. It is known that in such a setup the inertial term is essential for the emergence of negative mobility and it cannot be detected in the limiting case of overdamped dynamics. We analyse inertial effects and show that negative mobility can be observed even in the strong damping regime. We determine the optimal dimensionless mass for the presence of negative mobility and reveal three mechanisms standing behind this anomaly: deterministic chaotic, thermal noise induced and deterministic non-chaotic. The last origin has never been reported. It may provide guidance to the possibility of observation of negative mobility for strongly damped dynamics which is of fundamental importance from the point of view of biological systems, all of which in situ operate in fluctuating environments.

  1. Treadmilling of actin filaments via Brownian dynamics simulations

    Science.gov (United States)

    Guo, Kunkun; Shillcock, Julian; Lipowsky, Reinhard

    2010-10-01

    Actin polymerization is coupled to the hydrolysis of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and inorganic phosphate (Pi). Therefore, each protomer within an actin filament can attain three different nucleotide states corresponding to bound ATP, ADP/Pi, and ADP. These protomer states form spatial patterns on the growing (or shrinking) filaments. Using Brownian dynamics simulations, the growth behavior of long filaments is studied, together with the associated protomer patterns, as a function of ATP-actin monomer concentration, CT, within the surrounding solution. For concentrations close to the critical concentration CT=CT,cr, the filaments undergo treadmilling, i.e., they grow at the barbed and shrink at the pointed end, which leads to directed translational motion of the whole filament. The corresponding nonequilibrium states are characterized by several global fluxes and by spatial density and flux profiles along the filaments. We focus on a certain set of transition rates as deduced from in vitro experiments and find that the associated treadmilling (or turnover) rate is about 0.08 monomers per second.

  2. From Brownian Dynamics to Markov Chain: An Ion Channel Example

    KAUST Repository

    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.

  3. Beyond multifractional Brownian motion: new stochastic models for geophysical modelling

    Directory of Open Access Journals (Sweden)

    J. Lévy Véhel

    2013-09-01

    Full Text Available Multifractional Brownian motion (mBm has proved to be a useful tool in various areas of geophysical modelling. Although a versatile model, mBm is of course not always an adequate one. We present in this work several other stochastic processes which could potentially be useful in geophysics. The first alternative type is that of self-regulating processes: these are models where the local regularity is a function of the amplitude, in contrast to mBm where it is tuned exogenously. We demonstrate the relevance of such models for digital elevation maps and for temperature records. We also briefly describe two other types of alternative processes, which are the counterparts of mBm and of self-regulating processes when the intensity of local jumps is considered in lieu of local regularity: multistable processes allow one to prescribe the local intensity of jumps in space/time, while this intensity is governed by the amplitude for self-stabilizing processes.

  4. Beyond multifractional Brownian motion: new stochastic models for geophysical modelling

    Science.gov (United States)

    Lévy Véhel, J.

    2013-09-01

    Multifractional Brownian motion (mBm) has proved to be a useful tool in various areas of geophysical modelling. Although a versatile model, mBm is of course not always an adequate one. We present in this work several other stochastic processes which could potentially be useful in geophysics. The first alternative type is that of self-regulating processes: these are models where the local regularity is a function of the amplitude, in contrast to mBm where it is tuned exogenously. We demonstrate the relevance of such models for digital elevation maps and for temperature records. We also briefly describe two other types of alternative processes, which are the counterparts of mBm and of self-regulating processes when the intensity of local jumps is considered in lieu of local regularity: multistable processes allow one to prescribe the local intensity of jumps in space/time, while this intensity is governed by the amplitude for self-stabilizing processes.

  5. Characterizing Detrended Fluctuation Analysis of multifractional Brownian motion

    Science.gov (United States)

    Setty, V. A.; Sharma, A. S.

    2015-02-01

    The Hurst exponent (H) is widely used to quantify long range dependence in time series data and is estimated using several well known techniques. Recognizing its ability to remove trends the Detrended Fluctuation Analysis (DFA) is used extensively to estimate a Hurst exponent in non-stationary data. Multifractional Brownian motion (mBm) broadly encompasses a set of models of non-stationary data exhibiting time varying Hurst exponents, H(t) as against a constant H. Recently, there has been a growing interest in time dependence of H(t) and sliding window techniques have been used to estimate a local time average of the exponent. This brought to fore the ability of DFA to estimate scaling exponents in systems with time varying H(t) , such as mBm. This paper characterizes the performance of DFA on mBm data with linearly varying H(t) and further test the robustness of estimated time average with respect to data and technique related parameters. Our results serve as a bench-mark for using DFA as a sliding window estimator to obtain H(t) from time series data.

  6. Biased Brownian motion in narrow channels with asymmetry and anisotropy

    Science.gov (United States)

    To, Kiwing; Peng, Zheng

    2016-11-01

    We study Brownian motion of a single millimeter size bead confined in a quasi-two-dimensional horizontal channel with built-in anisotropy and asymmetry. Channel asymmetry is implemented by ratchet walls while anisotropy is introduced using a channel base that is grooved along the channel axis so that a bead can acquire a horizontal impulse perpendicular to the longitudinal direction when it collides with the base. When energy is injected to the channel by vertical vibration, the combination of asymmetric walls and anisotropic base induces an effective force which drives the bead into biased diffusive motion along the channel axis with diffusivity and drift velocity increase with vibration strength. The magnitude of this driving force, which can be measured in experiments of tilted channel, is found to be consistent to those obtained from dynamic mobility and position probability distribution measurements. These results are explained by a simple collision model that suggests the random kinetic energies transfer between different translational degrees of freedom may be turned into useful work in the presence of asymmetry and anisotropy.

  7. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    D)> HBr (0.83 D) > HI (0.45 D) [8]. Hence, these molecules can and do induce a dipole moment in the rare gas atoms when the two interact. The induced dipole moment is proportional to the inducing field E and the proportionality constant is the polariz- ability, i.e., μ i. = αE. However, as mentioned above, dispersion.

  8. UNIQUAC interaction parameters for molecules with -OH groups on adjacent carbon atoms in aqueous solution determined by molecular mechanics - glycols, glycerol and glucose

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Klein, R. A.

    1997-01-01

    Procedure (BJP).The predicted vapor-liquid-equilibrium (VLE) data for the water/1,2-ethanediol system are in excellent agreement with the experimentalvalues and good results were obtained for the water/glycerol system by taking larger samples. This was not true for the other two systemsfor which there were...... difficulties in sampling conformational space in a statistically acceptable manner. As the parameters representinteractions per unit molecular surface area and all of the molecules consist of -CH2OH or -CH2O- units, the values obtained for thewater/1,2-ethanediol system were used to predict VLE data...... for the other systems. This gave results in good agreement with the experimental data.The possibility of transferring interaction parameters is very interesting,especially as it can be applied to systems for which the additivity principle of the UNIFAC method fails.Simulations were carried out for 1...

  9. Relaxed electric dipole moments of polar molecules interacting with a slow positron: H{sub 2}O and CH{sub 3}X (X=F, Cl, Br)

    Energy Technology Data Exchange (ETDEWEB)

    Assafrao, Denise; Mohallem, Jose R, E-mail: rachid@fisica.ufmg.b [Laboratorio de Atomos e Moleculas Especiais, Departamento de FIsica, ICEx, Universidade Federal de Minas Gerais, PO Box 702, 30123-970, Belo Horizonte, MG (Brazil)

    2010-08-14

    The variation in the electric dipole moments of H{sub 2}O, CH{sub 3}F, CH{sub 3}Cl and CH{sub 3}Br as their geometries relax due to interaction with a positron is evaluated. The results are in good agreement with a recently observed empirical dependence of the positron binding energy on molecular properties (Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203). For binding energies larger than 100 meV relaxation could alter significantly the analysis of the binding, but it is in the prospect of generating effective potentials for positron scattering by molecules that the effect can be more important.

  10. Translocation of a Polymer Chain across a Nanopore: A Brownian Dynamics Simulation Study

    Science.gov (United States)

    Tian, Pu; Smith, Grant D.

    2003-01-01

    We carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient). The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient across the wall), we focused on the latter case in our studies. Calculation of radius of gyrations at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tubelike pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied, attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.

  11. Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

    Science.gov (United States)

    Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.

    2011-08-01

    Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.

  12. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip

    2007-01-01

    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  13. TM14 is a new member of the fibulin family (fibulin-7) that interacts with extracellular matrix molecules and is active for cell binding.

    Science.gov (United States)

    de Vega, Susana; Iwamoto, Tsutomu; Nakamura, Takashi; Hozumi, Kentaro; McKnight, Dianalee A; Fisher, Larry W; Fukumoto, Satoshi; Yamada, Yoshihiko

    2007-10-19

    We identified a new extracellular protein, TM14, by differential hybridization using mouse tooth germ cDNA microarrays. TM14 cDNA encodes 440 amino acids containing a signal peptide. The protein contains 3 EGF modules at the center, a C-terminal domain homologous to the fibulin module, and a unique Sushi domain at the N terminus. In situ hybridization revealed that TM14 mRNA was expressed by preodontoblasts and odontoblasts in developing teeth. TM14 mRNA was also expressed in cartilage, hair follicles, and extraembryonic tissues of the placenta. Immunostaining revealed that TM14 was localized at the apical pericellular regions of preodontoblasts. When the dentin matrix was fully formed and dentin mineralization occurred, TM14 was present in the predentin matrix and along the dentinal tubules. We found that the recombinant TM14 protein was glycosylated with N-linked oligosaccharides and interacted with heparin, fibronectin, fibulin-1, and dentin sialophosphoprotein. We also found that TM14 preferentially bound dental mesenchyme cells and odontoblasts but not dental epithelial cells or nondental cells such as HeLa, COS7, or NIH3T3 cells. Heparin, EDTA, and anti-integrin beta1 antibody inhibited TM14 binding to dental mesenchyme cells, suggesting that both a heparan sulfate-containing cell surface receptor and an integrin are involved in TM14 cell binding. Our findings indicate that TM14 is a cell adhesion molecule that interacts with extracellular matrix molecules in teeth and suggest that TM14 plays important roles in both the differentiation and maintenance of odontoblasts as well as in dentin formation. Because of its protein characteristics, TM14 can be classified as a new member of the fibulin family: fibulin-7.

  14. Stability of defects in monolayer MoS{sub 2} and their interaction with O{sub 2} molecule: A first-principles study

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, B. [Hubei Nuclear Solid Physics Key Laboratory, Department of Physics, Wuhan University, Wuhan, 430072 (China); Shang, C. [Wuhan National High Magnetic Field Center, Huazhong University of Science and Technology, Wuhan, 430074 (China); Qi, N. [Hubei Nuclear Solid Physics Key Laboratory, Department of Physics, Wuhan University, Wuhan, 430072 (China); Chen, Z.Y. [School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning, 437100 (China); Chen, Z.Q., E-mail: chenzq@whu.edu.cn [Hubei Nuclear Solid Physics Key Laboratory, Department of Physics, Wuhan University, Wuhan, 430072 (China)

    2017-08-01

    Highlights: • Defects can exist steadily in monolayer MoS{sub 2} and break surface chemical inertness. • Activated surfaces are beneficial to the adsorption of O{sub 2} through the introduction of defect levels. • Adsorbed O{sub 2} on defective surface can dissociate with low activation energy barrier. • Defective system may be a potential substrate to design MoS{sub 2}-based gas sensor or catalysts. - Abstract: The stability of various defects in monolayer MoS{sub 2}, as well as their interactions with free O{sub 2} molecules were investigated by density functional theory (DFT) calculations coupled with the nudged elastic band (NEB) method. The defects including S vacancy (monosulfur and disulfue vacancies), antisite defect (Mo{sub S}) and external Mo atom can exist steadily in monolayer MoS{sub 2}, and introduce defect levels in these defective systems, which breaks the surface chemical inertness and significantly enhances the adsorption capacity for free O{sub 2}. The adsorption energy calculations and electronic properties analysis suggest that there is a strong interaction between O{sub 2} molecule and defective system. The adsorbed O{sub 2} on the defective surface can dissociate with a lower activation energy barrier, which produce two active oxygen atoms. Especially, two Mo atoms can occupy one Mo lattice site, and adsorbed O{sub 2} on the top of the Mo atom can then dissociate directly with the lowest activation energy barrier. Hence, our work may provide useful information to design MoS{sub 2}-based gas sensor or catalysts.

  15. Rotationally adiabatic pair interactions of para- and ortho-hydrogen with the halogen molecules F2, Cl2, and Br2.

    Science.gov (United States)

    Berg, Matthias; Accardi, Antonio; Paulus, Beate; Schmidt, Burkhard

    2014-08-21

    The present work is concerned with the weak interactions between hydrogen and halogen molecules, i.e., the interactions of pairs H2-X2 with X = F, Cl, Br, which are dominated by dispersion and quadrupole-quadrupole forces. The global minimum of the four-dimensional (4D) coupled cluster with singles and doubles and perturbative triples (CCSD(T)) pair potentials is always a T shaped structure where H2 acts as the hat of the T, with well depths (De) of 1.3, 2.4, and 3.1 kJ/mol for F2, Cl2, and Br2, respectively. MP2/AVQZ results, in reasonable agreement with CCSD(T) results extrapolated to the basis set limit, are used for detailed scans of the potentials. Due to the large difference in the rotational constants of the monomers, in the adiabatic approximation, one can solve the rotational Schrödinger equation for H2 in the potential of the X2 molecule. This yields effective two-dimensional rotationally adiabatic potential energy surfaces where pH2 and oH2 are point-like particles. These potentials for the H2-X2 complexes have global and local minima for effective linear and T-shaped complexes, respectively, which are separated by 0.4-1.0 kJ/mol, where oH2 binds stronger than pH2 to X2, due to higher alignment to minima structures of the 4D-pair potential. Further, we provide fits of an analytical function to the rotationally adiabatic potentials.

  16. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    Science.gov (United States)

    Kanada, Ryo; Kuwata, Takeshi; Kenzaki, Hiroo; Takada, Shoji

    2013-01-01

    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."

  17. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    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."

  18. Small molecule inhibitors uncover synthetic genetic interactions of human flap endonuclease 1 (FEN1 with DNA damage response genes.

    Directory of Open Access Journals (Sweden)

    Thomas A Ward

    Full Text Available Flap endonuclease 1 (FEN1 is a structure selective endonuclease required for proficient DNA replication and the repair of DNA damage. Cellularly active inhibitors of this enzyme have previously been shown to induce a DNA damage response and, ultimately, cell death. High-throughput screens of human cancer cell-lines identify colorectal and gastric cell-lines with microsatellite instability (MSI as enriched for cellular sensitivity to N-hydroxyurea series inhibitors of FEN1, but not the PARP inhibitor olaparib or other inhibitors of the DNA damage response. This sensitivity is due to a synthetic lethal interaction between FEN1 and MRE11A, which is often mutated in MSI cancers through instabilities at a poly(T microsatellite repeat. Disruption of ATM is similarly synthetic lethal with FEN1 inhibition, suggesting that disruption of FEN1 function leads to the accumulation of DNA double-strand breaks. These are likely a result of the accumulation of aberrant replication forks, that accumulate as a consequence of a failure in Okazaki fragment maturation, as inhibition of FEN1 is toxic in cells disrupted for the Fanconi anemia pathway and post-replication repair. Furthermore, RAD51 foci accumulate as a consequence of FEN1 inhibition and the toxicity of FEN1 inhibitors increases in cells disrupted for the homologous recombination pathway, suggesting a role for homologous recombination in the resolution of damage induced by FEN1 inhibition. Finally, FEN1 appears to be required for the repair of damage induced by olaparib and cisplatin within the Fanconi anemia pathway, and may play a role in the repair of damage associated with its own disruption.

  19. Brownian Motion Problem: Random Walk and Beyond -RE ...

    Indian Academy of Sciences (India)

    by their continuous bombardment by the surrounding molecules of much smaller size (Figure 1). This effect .... of continuous impacts of the randomly moving surround- ing molecules of the fluid (the 'npise'); (ii) these ..... ually increasing range of values due to integration and, thus, keeping it alive. Consequently, the observed ...

  20. Double-edged swords as cancer therapeutics: novel, orally active, small molecules simultaneously inhibit p53-MDM2 interaction and the NF-κB pathway.

    Science.gov (United States)

    Zhuang, Chunlin; Miao, Zhenyuan; Wu, Yuelin; Guo, Zizhao; Li, Jin; Yao, Jianzhong; Xing, Chengguo; Sheng, Chunquan; Zhang, Wannian

    2014-02-13

    Simultaneous inactivation of p53 and hyperactivation of nuclear factor-κB (NF-κB) is a common occurrence in human cancer. Currently, antitumor agents are being designed to selectively activate p53 or inhibit NF-κB. However, there is no concerted effort yet to deliberately design inhibitors that can simultaneously do both. This paper provided a proof-of-concept study that p53-MDM2 interaction and NF-κB pathway can be simultaneously targeted by a small-molecule inhibitor. A series of pyrrolo[3,4-c]pyrazole derivatives were rationally designed and synthesized as the first-in-class inhibitors of p53-MDM2 interaction and NF-κB pathway. Most of the compounds were identified to possess nanomolar p53-MDM2 inhibitory activity. Compounds 5q and 5s suppressed NF-κB activation through inhibition of IκBα phosphorylation and elevation of the cytoplasmic levels of p65 and phosphorylated IKKα/β. Biochemical assay for the kinases also supported the fact that pyrrolo[3,4-c]pyrazole compounds directly targeted the NF-κB pathway. In addition, four compounds (5j, 5q, 5s, and 5u) effectively inhibited tumor growth in the A549 xenograft model. Further pharmacokinetic study revealed that compound 5q exhibited excellent oral bioavailability (72.9%).