Nevena Ilieva

Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example

We inquire how structure emerges during the process of protein folding. For this we scrutinize collective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop, and employ various topological techniques, in combination with analytic tools that we deduce from the concept of integrable models and structure of discrete nonlinear Schrödinger equation. The example we consider is an α-helical subunit of the HIV envelope glycoprotein gp41. The helical structure is stable when the subunit is part of the biological oligomer. But in isolation, the helix becomes unstable, and the monomer starts deforming. We follow the process computationally. We interpret the evolving structure both in terms of a backbone based Heisenberg spin chain and in terms of a side chain based XY spin chain. We find that in both cases the formation of protein supersecondary structure is akin the formation of a topological Bloch domain wall along a spin chain. During the process we identify three individual Bloch walls and we show that each of them can be modelled with a precision of tenths to several angstroms in terms of a soliton solution to a discrete nonlinear Schrödinger equation.

Multigap RPC for PET: development and optimisation of the detector design

Transforming the resistive plate chambers from charged-particle into gamma-quanta detectors opens the way towards their application as a basic element of a hybrid imaging system, which combines positron emission tomography (PET) with magnetic resonance imaging (MRI) in a single device and provides non- and minimally- invasive quantitative methods for diagnostics. To this end, we performed detailed investigations encompassing the whole chain from the annihilation of the positron in the body, through the conversion of the created photons into electrons and to the optimization of the electron yield in the gas. GEANT4 based simulations of the efficiency of the RPC photon detectors with different converter materials and geometry were conducted for optimization of the detector design. The results justify the selection of a sandwich-type gas-insulator-converter design, with Bi or Pb as converter materials.

Supersymmetric Models for Fermions on a Lattice

We investigate the large-N behaviour of simple examples of supersymmetric interactions for fermions on a lattice. Witten’s supersymmetric quantum mechanics and the BCS model appear just as two different aspects of one and the same model. For the BCS model, supersymmetry is only respected in a coherent superposition of Bogoliubov states. In this coherent superposition mesoscopic observables show better stability properties than in a Bogoliubov state.

DIRAC VARIABLES AND ZERO MODES OF GAUSS CONSTRAINT IN FINITE-VOLUME TWO-DIMENSIONAL QED

The finite-volume QED1+1 is formulated in terms of Dirac variables by an explicit solution of the Gauss constraint with possible nontrivial boundary conditions taken into account. The intrinsic nontrivial topology of the gauge group is thus revealed together with its zero-mode residual dynamics. Topologically nontrivial gauge transformations generate collective excitations of the gauge field above Colemans ground state, that are completely decoupled from local dynamics, the latter being equivalent to a free massive scalar field theory.

Do anyons solve Heisenberg's Urgleichung in one dimension

Abstract. We construct solutions to the chiral Thirring model in the framework of algebraic quantum field theory. We find that for all positive temperatures there are fermionic solutions only if the coupling constant is

Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example

\lambda = \sqrt{2(2n+1)\pi}, \, n\in \bf N

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

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Thermal correlators of anyons in two dimensions

We propose to combine a mean-field approach with all-atom molecular dynamics (MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques. We argue that a room-temperature monomeric Myc is in a dynamical state, it oscillates between different conformations that we identify. For this we adopt the Cα backbone of Myc in a crystallographic heteromer as an initial ansatz for the monomeric structure. We construct a multisoliton of the pertinent Landau free energy to describe the Cα profile with ultrahigh precision. We use Glauber dynamics to resolve how the multisoliton responds to repeated increases and decreases in ambient temperature. We confirm that the initial structure is unstable in isolation. We reveal a highly degenerate ground-state landscape, an attractive set towards which Glauber dynamics converges in the limit of vanishing ambient temperature. We analyze the thermal stability of this Glauber attractor using room-temperature molecular dynamics. We identify and scrutinize a particularly stable subset in which the two helical segments of the original multisoliton align in parallel next to each other. During the MD time evolution of a representative structure from this subset, we observe intermittent quasiparticle oscillations along the C-terminal α helix, some of which resemble a translating Davydovs Amide-I soliton. We propose that the presence of oscillatory motion is in line with the expected intrinsically disordered character of Myc.

Finding semirigid domains in biomolecules by clustering pair-distance variations.

Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.

TWO-DIMENSIONAL ANYONS AND THE TEMPERATURE DEPENDENCE OF COMMUTATOR ANOMALIES

The anyon fields have a trivial α-commutator for α not integer. For integer α the commutators become temperature-dependent operator-valued distributions. The n-point functions do not factorize as for quasifree states.