0000000000116651
AUTHOR
Thomas Kühn
showing 15 related works from this author
Computational Modeling of Protein Dynamics in Eukaryotic Cells
2012
Proteins have important functions inside the cell, traveling diffusively or being actively transported to various cellular sites where their activity is needed. Protein motion in the cellular environment is therefore an important topic to understand. However, the cell provides a very complex environment for that motion, which poses problems especially for any modeling effort designed to interpret experimentally observed features. So as to gain a realistic picture of protein dynamics inside the cell, we have recently introduced advanced numerical methods for describing that dynamics [1]. The starting point is an accurate numerical duplicate of the cell determined by LSCM, which can be used a…
Protein diffusion in mammalian cell cytoplasm.
2011
We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribut…
Quantization of the elastic modes in an isotropic plate
2006
We quantize the elastic modes in a plate. For this, we find a complete, orthogonal set of eigenfunctions of the elastic equations and we normalize them. These are the phonon modes in the plate and their specific forms and dispersion relations are manifested in low temperature experiments in ultra-thin membranes.
Method for finding the critical temperature of the island in a SET structure
2008
We present a method to measure the critical temperature of the island of a superconducting single electron transistor. The method is based on a sharp change in the slope of the zero-bias conductance as a function of temperature. We have used this method to determine the superconducting phase transition temperature of the Nb island of an superconducting single electron transistor with Al leads. We obtain $T_\mathrm{c}^\mathrm{Nb}$ as high as 8.5 K and gap energies up to $\Delta_\mathrm{Nb}\simeq 1.45$ meV. By looking at the zero bias conductance as a function of magnetic field instead of temperature, also the critical field of the island can be determined. Using the orthodox theory, we have …
Electronic and Thermal Sequential Transport in Metallic and Superconducting Two-Junction Arrays
2010
The description of transport phenomena in devices consisting of arrays of tunnel junctions, and the experimental confirmation of these predictions is one of the great successes of mesoscopic physics. The aim of this paper is to give a self-consistent review of sequential transport processes in such devices, based on the so-called “orthodox” model. We calculate numerically the current-voltage (I–V) curves, the conductance versus bias voltage (G–V) curves, and the associated thermal transport in symmetric and asymmetric two-junction arrays such as Coulomb-blockade thermometers (CBTs), superconducting-insulator-normal-insulator-superconducting (SINIS) structures, and superconducting single-ele…
Chromatin organization regulates viral egress dynamics.
2017
Various types of DNA viruses are known to elicit the formation of a large nuclear viral replication compartment and marginalization of the cell chromatin. We used three-dimensional soft x-ray tomography, confocal and electron microscopy, combined with numerical modelling of capsid diffusion to analyse the molecular organization of chromatin in herpes simplex virus 1 infection and its effect on the transport of progeny viral capsids to the nuclear envelope. Our data showed that the formation of the viral replication compartment at late infection resulted in the enrichment of heterochromatin in the nuclear periphery accompanied by the compaction of chromatin. Random walk modelling of herpes s…
Response of Vertisols, Andosols, and Alisols to paddy management
2016
Abstract Interchanging submergence and drainage in paddy soils induce alternating redox conditions. It is known that this causes changes in organic carbon stocks, in amounts and crystallinity of Fe oxides as well as transformation of clay minerals and subsequent changes in cation exchange capacity (CEC). However, the influence of the initial soil type on the extent of these changes is not yet well understood. Therefore, we studied paddy soils that derived from three different soil types (Vertisols, Andosols, Alisols) on volcanic parent material in Java (Indonesia). To account for the variability in parent materials, we additionally sampled sandstone-derived Alisols in China. Adjacent non-pa…
Cooper-pair resonances and subgap Coulomb blockade in a superconducting single-electron transistor
2003
We have fabricated and measured superconducting single-electron transistors with Al leads and Nb islands. At bias voltages below the gap of Nb we observe clear signatures of resonant tunneling of Cooper pairs, and of Coulomb blockade of the subgap currents due to linewidth broadening of the energy levels in the superconducting density of states of Nb. The experimental results are in good agreement with numerical simulations.
Interaction of two-level systems in amorphous materials with arbitrary phonon fields
2006
To describe the interaction of the two level systems (TLSs) of an amorphous solid with arbitrary strain fields, we introduce a generalization of the standard interaction Hamiltonian. In this new model, the interaction strength depends on the orientation of the TLS with respect to the strain field through a $6\times 6$ symmetric tensor of deformation potential parameters, $[R]$. Taking into account the isotropy of the amorphous solid, we deduce that $[R]$ has only two independent parameters. We show how these two parameters can be calculated from experimental data and we prove that for any amorphous bulk material the average coupling of TLSs with longitudinal phonons is always stronger than …
Ballistic phonon transport in dielectric membranes
2006
We have calculated the ballistic phononic heat transport in dielectric membranes as a function of radiator temperature and membrane thickness. The phonon modes of such membranes are known as Lamb-modes from elasticity theory. The striking result is that, for a fixed temperature, the radiated power first decreases with decreasing membrane thickness, but then develops a minimum when the transition to two dimensionality is reached. Further decrease of the membrane thickness in the 2D limit leads to increasing radiated power.
Diffusion through thin membranes: Modeling across scales
2016
From macroscopic to microscopic scales it is demonstrated that diffusion through membranes can be modeled using specific boundary conditions across them. The membranes are here considered thin in comparison to the overall size of the system. In a macroscopic scale the membrane is introduced as a transmission boundary condition, which enables an effective modeling of systems that involve multiple scales. In a mesoscopic scale, a numerical lattice-Boltzmann scheme with a partial-bounceback condition at the membrane is proposed and analyzed. It is shown that this mesoscopic approach provides a consistent approximation of the transmission boundary condition. Furthermore, analysis of the mesosco…
Modeling of Particle Number Fluctuations in Entire Cells
2012
In a recent study we developed a method to model protein diffusion in cells [1], where special attention was given to generating from image data of the measured cell a realistic digital model cell in which protein dynamics were simulated. The method was shown to be well suited for modeling non-equilibrium situations that arise, e.g., in photobleaching experiments, and to be capable of producing more detailed information about protein motion than traditional modeling.Another experimental way to assess protein dynamics is to study fluctuations in the local protein number, as it is done, e.g., in fluorescence correlation spectroscopy (FCS), or in similar measurements that apply single-plane il…
Interaction of Lamb modes with two-level systems in amorphous nanoscopic membranes
2007
Using a generalized model of interaction between a two-level system (TLS) and an arbitrary deformation of the material, we calculate the interaction of Lamb modes with TLSs in amorphous nanoscopic membranes. We compare the mean free paths of the Lamb modes with different symmetries and calculate the heat conductivity $\kappa$. In the limit of an infinitely wide membrane, the heat conductivity is divergent. Nevertheless, the finite size of the membrane imposes a lower cut-off for the phonons frequencies, which leads to the temperature dependence $\kappa\propto T(a+b\ln T)$. This temperature dependence is a hallmark of the TLS-limited heat conductance at low temperature.
The tensor of interaction of a two-level system with an arbitrary strain field
2007
The interaction between two-level systems (TLS) and strain fields in a solid is contained in the diagonal matrix element of the interaction hamiltonian, $\delta$, which, in general, has the expression $\delta=2[\gamma]:[S]$, with the tensor $[\gamma]$ describing the TLS ``deformability'' and $[S]$ being the symmetric strain tensor. We construct $[\gamma]$ on very general grounds, by associating to the TLS two objects: a direction, $\hat\bt$, and a forth rank tensor of coupling constants, $[[R]]$. Based on the method of construction and on the invariance of the expression of $\delta$ with respect to the symmetry transformation of the solid, we conclude that $[[R]]$ has the same structure as …
Maximizing phonon thermal conductance for ballistic membranes
2007
At low temperatures, phonon scattering can become so weak that phonon transport becomes ballistic. We calculate the ballistic phonon conductance G for membranes using elasticity theory, considering the transition from three to two dimensions. We discuss the temperature and thickness dependence and especially concentrate on the issue of material parameters. For all membrane thicknesses, the best conductors have, counter-intuitively, the lowest speed of sound.