arXiv subjects

Tihamer Geyer

Publications and source records attributed to Tihamer Geyer.

9 recordsLinked to original sources

arXiv2009

Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions

In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong that the particles' velocities are damped much faster than the duration of an integration timestep. Here we show that this conceptual limit can be dropped with an analytic integration of the equations of damped motion. In the resulting Langevin integration scheme our recently proposed approximate form of the hydrodynamic interactions between the particles can be incorparated conveniently, leading to a fast multi-particle propagation scheme, which captures more of the short-time and short-range solvent effects than standard BD. Comparing the dynamics of a bead-spring model of a short peptide, we recommend to run simulations of small biological molecules with the Langevin type finite damping and to include the hydrodynamic interactions.

q-bio.BM↗

arXiv2008

An O(N^2) Approximation for Hydrodynamic Interactions in Brownian Dynamics Simulations

In the Ermak-McCammon algorithm for Brownian Dynamics, the hydrodynamic interactions (HI) between N spherical particles are described by a 3N x 3N diffusion tensor. This tensor has to be factorized at each timestep with a runtime of O(N^3), making the calculation of the correlated random displacements the bottleneck for many-particle simulations. Here we present a faster algorithm for this step, which is based on a truncated expansion of the hydrodynamic multi-particle correlations as two-body contributions. The comparison to the exact algorithm and to the Chebyshev approximation of Fixman verifies that for bead-spring polymers this approximation yields about 95% of the hydrodynamic correlations at an improved runtime scaling of O(N^2) and a reduced memory footprint. The approximation is independent of the actual form of the hydrodynamic tensor and can be applied to arbitrary particle configurations. This now allows to include HI into large many-particle Brownian dynamics simulations, where until now the runtime scaling of the correlated random motion was prohibitive.

cond-mat.soft↗

arXiv2007

Form follows function -- how PufX increases the efficiency of the light-harvesting complexes of Rhodobacter sphaeroides

Some species of purple bacteria as, e.g., Rhodobacter sphaeroides contain the protein PufX. Concurrently, the light harvesting complexes 1 (LH1) form dimers of open rings. In mutants without PufX, the LH1s are closed rings and photosynthesis breaks down, because the ubiquinone exchange at the reaction center is blocked. Thus, PufX is regarded essential for quinone exchange. In contrast to this view, which implicitly treats the LH1s as obstacles to photosynthesis, we propose that the primary purpose of PufX is to improve the efficiency of light harvesting by inducing the LH1 dimerization. Calculations with a dipole model, which compare the photosynthetic efficiency of various configurations of monomeric and dimeric core complexes, show that the dimer can absorb photons directly into the RC about 30% more efficient, when related to the number of bacteriochlorophylls, but that the performance of the more sophisticated dimeric LH1 antenna degrades faster with structural perturbations. The calculations predict an optimal orientation of the reaction centers relative to the LH1 dimer, which agrees well with the experimentally found configuration. For the increased required rigidity of the dimer additional modifications of the LH1 subunits are necessary, which would lead to the observed ubiquinone blockage, when PufX is missing.

q-bio.QM↗

arXiv2005

A mapping approach to synchronization in the "Zajfman trap". II: the observed bunch

We extend a recently introduced mapping model, which explains the bunching phenomenon in an ion beam resonator for two ions [Geyer, Tannor, J. Phys. B 37 (2004) 73], to describe the dynamics of the whole ion bunch. We calculate the time delay of the ions from a model of the bunch geometry and find that the bunch takes on a spherical form at the turning points in the electrostatic mirrors. From this condition we derive how the observed bunch length depends on the experimental parameters. We give an interpretation of the criteria for the existence of the bunch, which were derived from the experimental observations by Pedersen et al [Pedersen etal, Phys. Rev. A 65 042704].

physics.atom-ph↗

arXiv2003

Electron impact double ionization of helium from classical trajectory calculations

With a recently proposed quasiclassical ansatz [Geyer and Rost, J. Phys. B 35 (2002) 1479] it is possible to perform classical trajectory ionization calculations on many electron targets. The autoionization of the target is prevented by a Møller type backward--forward propagation scheme and allows to consider all interactions between all particles without additional stabilization. The application of the quasiclassical ansatz for helium targets is explained and total and partially differential cross sections for electron impact double ionization are calculated. In the high energy regime the classical description fails to describe the dominant TS1 process, which leads to big deviations, whereas for low energies the total cross section is reproduced well. Differential cross sections calculated at 250 eV await their experimental confirmation.

physics.atom-ph↗

arXiv2002

Dynamical stabilization of classical multi electron targets against autoionization

We demonstrate that a recently published quasiclassical M\oller type approach [Geyer and Rost 2002, J. Phys. B 35 1479] can be used to overcome the problem of autoionization, which arises in classical trajectory calculations for many electron targets. In this method the target is stabilized dynamically by a backward--forward propagation scheme. We illustrate this refocusing and present total cross sections for single and double ionization of helium by electron impact.

physics.atom-ph↗

arXiv2002

A mapping approach to synchronization in the "Zajfman trap": stability conditions and the synchronization mechanism

We present a two particle model to explain the mechanism that stabilizes a bunch of positively charged ions in an "ion trap resonator" [Pedersen etal, Phys. Rev. Lett. 87 (2001) 055001]. The model decomposes the motion of the two ions into two mappings for the free motion in different parts of the trap and one for a compressing momentum kick. The ions' interaction is modelled by a time delay, which then changes the balance between adjacent momentum kicks. Through these mappings we identify the microscopic process that is responsible for synchronization and give the conditions for that regime.

physics.atom-ph↗

arXiv2001

A quasi classical approach to electron impact ionization

A quasi classical approximation to quantum mechanical scattering in the Moeller formalism is developed. While keeping the numerical advantage of a standard Classical--Trajectory--Monte--Carlo calculation, our approach is no longer restricted to use stationary initial distributions. This allows one to improve the results by using better suited initial phase space distributions than the microcanonical one and to gain insight into the collision mechanism by studying the influence of different initial distributions on the cross section. A comprehensive account of results for single, double and triple differential cross sections for atomic hydrogen will be given, in comparison with experiment and other theories.

physics.atom-ph↗

arXiv2000

A quasi classical approach to fully differential ionization cross sections

A classical approximation to time dependent quantum mechanical scattering in the Møller formalism is presented. Numerically, our approach is similar to a standard Classical-Trajectory-Monte-Carlo calculation. Conceptually, however, our formulation allows one to release the restriction to stationary initial distributions. This is achieved by a classical forward-backward propagation technique. As a first application and for comparison with experiment we present fully differential cross sections for electron impact ionization of atomic hydrogen in the Erhardt geometry.

physics.atom-ph↗