Marcin Kostur

Rectification in synthetic conical nanopores: A one-dimensional Poisson-Nernst-Planck model

Ion transport in biological and synthetic nanochannels is characterized by phenomena such as ion current fluctuations and rectification. Recently, it has been demonstrated that nanofabricated synthetic pores can mimic transport properties of biological ion channels [P. Yu. Apel, Nucl. Instrum Methods Phys. Res. B 184, 337 (2001); Z. Siwy, Europhys. Lett. 60, 349 (2002)]. Here, the ion current rectification is studied within a reduced one-dimensional (1D) Poisson-Nernst-Planck (PNP) model of synthetic nanopores. A conical channel of a few nm to a few hundred nm in diameter, and of a few mum long is considered in the limit where the channel length considerably exceeds the Debye screening length. The rigid channel wall is assumed to be weakly charged. A one-dimensional reduction of the three-dimensional problem in terms of corresponding entropic effects is put forward. The ion transport is described by the nonequilibrium steady-state solution of the 1D Poisson-Nernst-Planck system within a singular perturbation treatment. An analytic formula for the approximate rectification current in the lowest order perturbation theory is derived. A detailed comparison between numerical results and the singular perturbation theory is presented. The crucial importance of the asymmetry in the potential jumps at the pore ends on the rectification effect is demonstrated. This so constructed 1D theory is shown to describe well the experimental data in the regime of small-to-moderate electric currents.

Accelerating numerical solution of stochastic differential equations with CUDA

Numerical integration of stochastic dierential equations is commonly used in many branches of science. In this paper we present how to accelerate this kind of numerical calculations with popular NVIDIA Graphics Processing Units using the CUDA programming environment. We address general aspects of numerical programming on stream processors and illustrate them by two examples: the noisy phase dynamics in a Josephson junction and the noisy Kuramoto model. In presented cases the measured speedup can be as high as 675 compared to a typical CPU, which corresponds to several billion integration steps per second. This means that calculations which took weeks can now be completed in less than one hour. This brings stochastic simulation to a completely new level, opening for research a whole new range of problems which can now be solved interactively.

Flow profiling of a surface-acoustic-wave nanopump.

The flow profile in a capillary gap and the pumping efficiency of an acoustic micropump employing surface acoustic waves is investigated both experimentally and theoretically. Ultrasonic surface waves on a piezoelectric substrate strongly couple to a thin liquid layer and generate a quadrupolar streaming pattern within the fluid. We use fluorescence correlation spectroscopy and fluorescence microscopy as complementary tools to investigate the resulting flow profile. The velocity was found to depend on the applied power approximately linearly and to decrease with the inverse third power of the distance from the ultrasound generator on the chip. The found properties reveal acoustic streaming as a promising tool for the controlled agitation during microarray hybridization.

Absolute negative mobility induced by thermal equilibrium fluctuations

A novel transport phenomenon is identified that is induced by inertial Brownian particles which move in simple one-dimensional, symmetric periodic potentials under the influence of both a time periodic and a constant, biasing driving force. Within tailored parameter regimes, thermal equilibrium fluctuations induce the phenomenon of absolute negative mobility (ANM), which means that the particle noisily moves backwards against a small constant bias. When no thermal fluctuations act, the transport vanishes identically in these tailored regimes. ANM can also occur in the absence of fluctuations on grounds which are rooted solely in the complex, inertial deterministic dynamics. The experimental verification of this new transport scheme is elucidated for the archetype symmetric physical system: a convenient setup consisting of a resistively and capacitively shunted Josephson junction device.

Anticipated synchronization in coupled inertial ratchets with time-delayed feedback: A numerical study

We investigate anticipated synchronization between two periodically driven deterministic, dissipative inertial ratchets that are able to exhibit directed transport with a finite velocity. The two ratchets interact through a unidirectional delay coupling, one is acting as a master system while the other one represents the slave system. Each of the two dissipative deterministic ratchets is driven externally by a common periodic force. The delay coupling involves two parameters, the coupling strength and the (positive-valued) delay time. We study the synchronization features for the unbounded, current carrying trajectories of the master and the slave, respectively, for four different strengths of the driving amplitude. These in turn characterize differing phase space dynamics of the transporting ratchet dynamics, regular, intermittent and a chaotic transport regime. We find that the slave ratchet can respond in exactly the same way as the master will respond in the future, thereby anticipating the nonlinear directed transport.

Flow patterns and transport in Rayleigh surface acoustic wave streaming: combined finite element method and raytracing numerics versus experiments

This work presents an approach for determining the streaming patterns that are generated by Rayleigh surface acoustic waves in arbitrary 3-D geometries by finite element method (FEM) simulations. An efficient raytracing algorithm is applied on the acoustic subproblem to avoid the unbearable memory demands and computational time of a conventional FEM acoustics simulation in 3-D. The acoustic streaming interaction is modeled by a body force term in the Stokes equation. In comparisons between experiments and simulated flow patterns, we demonstrate the quality of the proposed technique.

Brownian motors: Current fluctuations and rectification efficiency

With this work, we investigate an often neglected aspect of Brownian motor transport, namely, the role of fluctuations of the noise-induced current and its consequences for the efficiency of rectifying noise. In doing so, we consider a Brownian inertial motor that is driven by an unbiased monochromatic, time-periodic force and thermal noise. Typically, we find that the asymptotic, time-, and noise-averaged transport velocities are small, possessing rather broad velocity fluctuations. This implies a corresponding poor performance for the rectification power. However, for tailored profiles of the ratchet potential and appropriate drive parameters, we can identify a drastic enhancement of the rectification efficiency. This regime is marked by persistent, unidirectional motion of the Brownian motor with few back-turns only. The corresponding asymmetric velocity distribution is then rather narrow, with a support that predominantly favors only one sign for the velocity.

Sailfish: A flexible multi-GPU implementation of the lattice Boltzmann method ☆

Abstract We present Sailfish, an open source fluid simulation package implementing the lattice Boltzmann method (LBM) on modern Graphics Processing Units (GPUs) using CUDA/OpenCL. We take a novel approach to GPU code implementation and use run-time code generation techniques and a high level programming language (Python) to achieve state of the art performance, while allowing easy experimentation with different LBM models and tuning for various types of hardware. We discuss the general design principles of the code, scaling to multiple GPUs in a distributed environment, as well as the GPU implementation and optimization of many different LBM models, both single component (BGK, MRT, ELBM) and multicomponent (Shan–Chen, free energy). The paper also presents results of performance benchmarks spanning the last three NVIDIA GPU generations (Tesla, Fermi, Kepler), which we hope will be useful for researchers working with this type of hardware and similar codes. Program Summary Program title: Sailfish Catalogue identifier: AETA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AETA_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU Lesser General Public License, version 3 No. of lines in distributed program, including test data, etc.: 225864 No. of bytes in distributed program, including test data, etc.: 46861049 Distribution format: tar.gz Programming language: Python, CUDA C, OpenCL. Computer: Any with an OpenCL or CUDA-compliant GPU. Operating system: No limits (tested on Linux and Mac OS X). RAM: Hundreds of megabytes to tens of gigabytes for typical cases. Classification: 12, 6.5. External routines: PyCUDA/PyOpenCL, Numpy, Mako, ZeroMQ (for multi-GPU simulations), scipy, sympy Nature of problem: GPU-accelerated simulation of single- and multi-component fluid flows. Solution method: A wide range of relaxation models (LBGK, MRT, regularized LB, ELBM, Shan–Chen, free energy, free surface) and boundary conditions within the lattice Boltzmann method framework. Simulations can be run in single or double precision using one or more GPUs. Restrictions: The lattice Boltzmann method works for low Mach number flows only. Unusual features: The actual numerical calculations run exclusively on GPUs. The numerical code is built dynamically at run-time in CUDA C or OpenCL, using templates and symbolic formulas. The high-level control of the simulation is maintained by a Python process. Additional comments: !!!!! The distribution file for this program is over 45 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: Problem-dependent, typically minutes (for small cases or short simulations) to hours (large cases or long simulations).

Chiral separation in microflows

Molecules that only differ by their chirality, so-called enantiomers, often possess different properties with respect to their biological function. Therefore, the separation of enantiomers presents a prominent challenge in molecular biology and has long been a main pursuit of organic chemistry. We suggest a new separation technique for chiral molecules that is based on the transport properties in a microfluidic flow with spatially variable vorticity. Because of their size the thermal fluctuating motion of the molecules must be taken into account. These fluctuations play a decisive role in the proposed separation mechanism.

Consistent description of quantum Brownian motors operating at strong friction.

A quantum Smoluchowski equation is put forward that consistently describes thermal quantum states. In particular, it notably does not induce a violation of the second law of thermodynamics. This so modified kinetic equation is applied to study {\it analytically} directed quantum transport at strong friction in arbitrarily shaped ratchet potentials that are driven by nonthermal two-state noise. Depending on the mutual interplay of quantum tunneling and quantum reflection these quantum corrections can induce both, either a sizable enhancement or a suppression of transport. Moreover, the threshold for current reversals becomes markedly shifted due to such quantum fluctuations.