The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

Carrier momentum relaxation in highly doped polar semiconductors and semiconductor heterostructures

Highly doped polar semiconductors are essential components of today’s semiconductor industry. Most strikingly, transistors in modern electronic devices are polar semiconductor heterostructures. It is important to thoroughly understand carrier transport in such structures. In doped polar semiconductors, collective excitations of the carriers (plasmons) and the atoms (polar phonons) couple. These coupled collective excitations affect the electrical conductivity, here quantified through the carrier mobility. In scattering events, the carriers and the coupled collective modes transfer momentum between each other. Carrier momentum transferred to polar phonons can be lost to other phonons through anharmonic decay, resulting in a finite carrier mobility. The plasmons do not have a decay mechanism which transfers carrier momentum irretrievably. Hence, carrier-plasmon scattering results in infinite carrier mobility. Momentum relaxation due to either carrier–plasmon scattering or carrier–polar-phonon scattering alone are well understood. However, only this thesis manages to treat momentum relaxation due to both scattering mechanisms on an equal footing, enabling us to properly calculate the mobility limited by carrier–coupled plasmon–polar phonon scattering. We achieved this by solving the coupled Boltzmann equations for the carriers and the collective excitations, focusing on the “drag” term and on the anharmonic decay process of the collective modes. Our approach uses dielectric functions to describe both the carrier-collective mode scattering and the decay of the collective modes. We applied our method to bulk polar semiconductors and heterostructures where various polar dielectrics surround a semiconducting monolayer of MoS2, where taking plasmons into account can increase the mobility by up to a factor 15 for certain parameters. This screening effect is up to 85% higher than if calculated with previous methods. To conclude, our approach provides insight into the momentum relaxation mechanism for carrier–coupled collective mode scattering, and better tools for calculating the screened polar phonon and interface polar phonon limited mobility.

Emerging modes of collective cell migration induced by geometrical constraints.

The role of geometrical confinement on collective cell migration has been recognized but has not been elucidated yet. Here, we show that the geometrical properties of the environment regulate the formation of collective cell migration patterns through cell-cell interactions. Using microfabrication techniques to allow epithelial cell sheets to migrate into strips whose width was varied from one up to several cell diameters, we identified the modes of collective migration in response to geometrical constraints. We observed that a decrease in the width of the strips is accompanied by an overall increase in the speed of the migrating cell sheet. Moreover, large-scale vortices over tens of cell lengths appeared in the wide strips whereas a contraction-elongation type of motion is observed in the narrow strips. Velocity fields and traction force signatures within the cellular population revealed migration modes with alternative pulling and/or pushing mechanisms that depend on extrinsic constraints. Force transmission through intercellular contacts plays a key role in this process because the disruption of cell-cell junctions abolishes directed collective migration and passive cell-cell adhesions tend to move the cells uniformly together independent of the geometry. Altogether, these findings not only demonstrate the existence of patterns of collective cell migration depending on external constraints but also provide a mechanical explanation for how large-scale interactions through cell-cell junctions can feed back to regulate the organization of migrating tissues.

Exploring the micro-politics of place: lifestyle migrants, collective identities and modes of belonging

Taking up Hopkins and Dixon’s (2006) call to attend to the micro-politics of everyday constructions of space and place, which necessarily involves psychological concepts such as identity, belonging and attachment, this paper aims to show how a critical socio-cognitive approach to discourse analysis is an effective means of unpacking the ways in which versions of place are (re)produced and negotiated through discursive practices, and in particular the ways in which ‘legitimate’ collective identities are constructed in relation to place. I focus on the contemporary social phenomenon of lifestyle migration. Within Europe, this typically involves relatively affluent northern Europeans moving to destinations in southern Europe that are strongly linked to tourism. Although lifestyle migrants are generally viewed by their hosts as ‘desirable’ migrants due to their perceived economic and socio-cultural capital, their integration into destination communities is often minimal. The question arises as to how these migrants construct modes of belonging in relation to their adopted home-place and how they relate to the other social groups with whom they share it. Using texts from a variety of sources, including in-depth interviews with British migrants in Portugal, I explore not only how migrants position themselves (and others) discursively in relation to places, but also how they are already positioned by discursive practices in the public sphere. I also examine to what extent the construction of a ‘legitimate’ mode of belonging involves the construction of intergroup cooperation within that place.

Collective excitations in coupled quantum wells

The dielectric response of a modulated three-dimensional electron system composed of a periodic array of quantum wells with weak coupling and strong coupling are studied, and the dispersions of the collective excitations and the single particle excitations as functions of wave vectors are given. It is found that for the nearly isolated multiple-quantum-well case with several subbands occupation, there is a three-dimensional-like plasmon when q(z)=0 (q(z) is the wave-vector component in the superlattice axis). There also exist intersubband collective excitations in addition to one intra-subband mode when q(z) not equal 0. The intra-subband mode has a linear dispersion relation with q(//) (the wave-vector component perpendicular to the superlattice axis) when q(//) is small. The inter-subband modes cover wider ranges in q(//) with increasing values of q(z). The energies of inter-subband collective excitations are close by the corresponding inter-subband single-particle excitation spectra. The collective excitation dispersions show obvious anisotropy in the 2D quantum limit. The calculated results agree with the experiment. The coupling between quantum wells affects markedly both the collective excitations and the single particle excitations spectra. The system shows gradually a near-three-dimensional electron gas character with increasing coupling. Copyright (C) 1996 Published by Elsevier Science Ltd

Nonlinear excitations in strongly-coupled plasma lattices: envelope solitons, kinks and intrinsic localized modes

Ensembles of charged particles (plasmas) are a highly complex form of matter, most often modeled as a many-body system characterized by weak inter-particle interactions (electrostatic coupling). However, strongly-coupled plasma configurations have recently been produced in laboratory, either by creating ultra-cold plasmas confined in a trap or by manipulating dusty plasmas in discharge experiments. In this paper, the nonlinear aspects involved in the motion of charged dust grains in a one-dimensional plasma monolayer (crystal) are discussed. Different types of collective excitations are reviewed, and characteristics and conditions for their occurrence in dusty plasma crystals are discussed, in a quasi-continuum approximation. Dust crystals are shown to support nonlinear kink-shaped supersonic solitary longitudinal excitations, as well as modulated envelope localized modes associated with longitudinal and transverse vibrations. Furthermore, the possibility for intrinsic localized modes (ILMs) — Discrete Breathers (DBs) — to occur is investigated, from first principles. The effect of mode-coupling is also briefly considered. The relation to previous results on atomic chains, and also to experimental results on strongly-coupled dust layers in gas discharge plasmas, is briefly discussed.

Collective excitations of trapped Bose-Einstein condensates in the energy and time domains

A time-dependent method for calculating the collective excitation frequencies and densities of a trapped, inhomogeneous Bose-Einstein condensate with circulation is presented. The results are compared with time-independent solutions of the Bogoliubov-de Gennes equations. The method is based on time-dependent linear-response theory combined with spectral analysis of moments of the excitation modes of interest. The technique is straightforward to apply, extremely efficient in our implementation with parallel fast Fourier transform methods, and produces highly accurate results. For high dimensionality or low symmetry the time-dependent approach is a more practical computational scheme and produces accurate and reliable data. The method is suitable for general trap geometries, condensate flows and condensates permeated with defects and vortex structures.

Computer simulation study of collective dynamics in the glass former Ca(NO3)(2)center dot 4H(2)O

Time correlation functions of current fluctuations were calculated by molecular dynamics (MD) simulations in order to investigate sound waves of high wavevectors in the glass-forming liquid Ca(NO3)(2)center dot 4H(2)O. Dispersion curves, omega(k), were obtained for longitudinal (LA) and transverse acoustic (TA) modes, and also for longitudinal optic (LO) modes. Spectra of LA modes calculated by MD simulations were modeled by a viscoelastic model within the memory function framework. The viscoelastic model is used to rationalize the change of slope taking place at k similar to 0.3 angstrom(-1) in the omega(k) curve of acoustic modes. For still larger wavevectors, mixing of acoustic and optic modes is observed. Partial time correlation functions of longitudinal mass currents were calculated separately for the ions and the water molecules. The wavevector dependence of excitation energies of the corresponding partial LA modes indicates the coexistence of a relatively stiff subsystem made of cations and anions, and a softer subsystem made of water molecules. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4751548]

Collective effects for the LHC injectors: non-ultrarelativistic approaches

The upgrade of the CERN accelerator complex has been planned in order to further increase the LHC performances in exploring new physics frontiers. One of the main limitations to the upgrade is represented by the collective instabilities. These are intensity dependent phenomena triggered by electromagnetic fields excited by the interaction of the beam with its surrounding. These fields are represented via wake fields in time domain or impedances in frequency domain. Impedances are usually studied assuming ultrarelativistic bunches while we mainly explored low and medium energy regimes in the LHC injector chain. In a non-ultrarelativistic framework we carried out a complete study of the impedance structure of the PSB which accelerates proton bunches up to 1.4 GeV. We measured the imaginary part of the impedance which creates betatron tune shift. We introduced a parabolic bunch model which together with dedicated measurements allowed us to point to the resistive wall impedance as the source of one of the main PSB instability. These results are particularly useful for the design of efficient transverse instability dampers. We developed a macroparticle code to study the effect of the space charge on intensity dependent instabilities. Carrying out the analysis of the bunch modes we proved that the damping effects caused by the space charge, which has been modelled with semi-analytical method and using symplectic high order schemes, can increase the bunch intensity threshold. Numerical libraries have been also developed in order to study, via numerical simulations of the bunches, the impedance of the whole CERN accelerator complex. On a different note, the experiment CNGS at CERN, requires high-intensity beams. We calculated the interpolating Hamiltonian of the beam for highly non-linear lattices. These calculations provide the ground for theoretical and numerical studies aiming to improve the CNGS beam extraction from the PS to the SPS.

Influence apart from Adoption: How Interaction between Programming and Scientific Practices Shapes Modes of Inquiry in Four Oceanography Teams

Thesis (Ph.D.)--University of Washington, 2016-06

REGULATION OF SHAPE DYNAMICS AND ACTIN POLYMERIZATION DURING COLLECTIVE CELL MIGRATION

This thesis aims to understand how cells coordinate their motion during collective migration. As previously shown, the motion of individually migrating cells is governed by wave-like cell shape dynamics. The mechanisms that regulate these dynamic behaviors in response to extracellular environment remain largely unclear. I applied shape dynamics analysis to Dictyostelium cells migrating in pairs and in multicellular streams and found that wave-like membrane protrusions are highly coupled between touching cells. I further characterized cell motion by using principle component analysis (PCA) to decompose complex cell shape changes into a serial shape change modes, from which I found that streaming cells exhibit localized anterior protrusion, termed front narrowing, to facilitate cell-cell coupling. I next explored cytoskeleton-based mechanisms of cell-cell coupling by measuring the dynamics of actin polymerization. Actin polymerization waves observed in individual cells were significantly suppressed in multicellular streams. Streaming cells exclusively produced F-actin at cell-cell contact regions, especially at cell fronts. I demonstrated that such restricted actin polymerization is associated with cell-cell coupling, as reducing actin polymerization with Latrunculin A leads to the assembly of F-actin at the side of streams, the decrease of front narrowing, and the decoupling of protrusion waves. My studies also suggest that collective migration is guided by cell-surface interactions. I examined the aggregation of Dictyostelim cells under distinct conditions and found that both chemical compositions of surfaces and surface-adhesion defects in cells result in altered collective migration patterns. I also investigated the shape dynamics of cells suspended on PEG-coated surfaces, which showed that coupling of protrusion waves disappears on touching suspended cells. These observations indicate that collective migration requires a balance between cell-cell and cell-surface adhesions. I hypothesized such a balance is reached via the regulation of cytoskeleton. Indeed, I found cells actively regulate cytoskeleton to retain optimal cell-surface adhesions on varying surfaces, and cells lacking the link between actin and surfaces (talin A) could not retain the optimal adhesions. On the other hand, suspended cells exhibited enhanced actin filament assembly on the periphery of cell groups instead of in cell-cell contact regions, which facilitates their aggregation in a clumping fashion.