arXiv subjects

Tapio Ala-Nissila

Publications and source records attributed to Tapio Ala-Nissila.

At least 91 records · Page 5Linked to original sources

arXiv2018

pH-Mediated Regulation of Polymer Transport Through SiN Pores

We characterize the pH controlled polymer capture and transport thorough silicon nitride (SiN) pores subject to protonation. A charge regulation model able to reproduce the experimental zeta potential of SiN pores is coupled with electrohydrodynamic polymer transport equations. The formalism can quantitatively explain the experimentally observed non-monotonic pH dependence of avidin conductivity in terms of the interplay between the electroosmotic and electrophoretic drag forces on the protein. We also scrutinize the DNA conductivity of SiN pores. We show that in the low pH regime where the amphoteric pore is cationic, DNA-pore attraction acts as an electrostatic trap. This provides a favorable condition for fast polymer capture and extended translocation required for accurate polymer sequencing.

cond-mat.soft↗

arXiv2018

Thermoplasmonic behavior of semiconductor nanoparticles: A comparison with metals

A number of applications in nanoplasmonics utilize noble metals, gold (Au) and silver (Ag), as the materials of choice. However, these materials suffer from problems of poor thermal and chemical stability accompanied by significant dissipative losses under high-temperature conditions. In this regard, semiconductor nanoparticles have attracted attention with their promising characteristics of highly tunable plasmonic resonances, low ohmic losses and greater thermochemical stability. Here, we investigate the size-dependent thermoplasmonic properties of semiconducting silicon and gallium arsenide nanoparticles to compare them with metallic Au nanoparticles using Mie theory. To this end, we employ experimentally estimated models of dielectric permittivity in our computations. Among the various permittivity models for Au, we further compare the Drude-Lorentz (DL) and the Drude and critical points (DCP) models. Results show a redshift in the scattering and absorption resonances for the DL model while the DCP model presents a blueshift. The dissipative damping in the semiconductor nanoparticles is strongest for the sharp electric octupole resonances followed by the quadrupole and dipole modes. However, a reverse order with strongest values for the broad dipole resonance is observed for the Au nanoparticles. A massive Drude broadening contributes strongly to the damping of resonances in Au nanoparticles at elevated temperatures. In contrast, the semiconductor nanoparticles do not exhibit any significant deterioration in their scattering and absorption resonances at high temperatures. In combination with low dissipative damping, this makes the semiconductor nanoparticles better suited for high-temperature applications in nanoplasmonics wherein the noble metals suffer from excessive heating.

cond-mat.mes-hall↗

arXiv2018

Grain extraction and microstructural analysis method for two-dimensional poly and quasicrystalline solids

While the microscopic structure of defected solid crystalline materials has significant impact on their physical properties, efficient and accurate determination of a given polycrystalline microstructure remains a challenge. In this paper we present a highly generalizable and reliable variational method to achieve this goal for two-dimensional crystalline and quasicrystalline materials. The method is benchmarked and optimized successfully using a variety of large-scale systems of defected solids, including periodic structures and quasicrystalline symmetries to quantify their microstructural characteristics, e.g., grain size and lattice misorientation distributions. We find that many microstructural properties show universal features independent of the underlying symmetries.

cond-mat.mtrl-sci↗

arXiv2018

Quantum Work in the Bohmian framework

At non-zero temperature classical systems exhibit statistical fluctuations of thermodynamic quantities arising from the variation of the system's initial conditions and its interaction with the environment. The fluctuating work, for example, is characterised by the ensemble of system trajectories in phase space and, by including the probabilities for various trajectories to occur, a work distribution can be constructed. However, without phase space trajectories, the task of constructing a work probability distribution in the quantum regime has proven elusive. Here we use quantum trajectories in phase space and define fluctuating work as power integrated along the trajectories, in complete analogy to classical statistical physics. The resulting work probability distribution is valid for any quantum evolution, including cases with coherences in the energy basis. We demonstrate the quantum work probability distribution and its properties with an exactly solvable example of a driven quantum harmonic oscillator. An important feature of the work distribution is its dependence on the initial statistical mixture of pure states, which is reflected in higher moments of the work. The proposed approach introduces a fundamentally different perspective on quantum thermodynamics, allowing full thermodynamic characterisation of the dynamics of quantum systems, including the measurement process.

quant-ph↗

arXiv2017

Flux-tunable heat sink for quantum electric circuits

Superconducting microwave circuits show great potential for practical quantum technological applications such as quantum information processing. However, fast and on-demand initialization of the quantum degrees of freedom in these devices remains a challenge. Here, we experimentally implement a tunable heat sink that is potentially suitable for the initialization of superconducting qubits. Our device consists of two coupled resonators. The first resonator has a high quality factor and a fixed frequency whereas the second resonator is designed to have a low quality factor and a tunable resonance frequency. We engineer the low quality factor using an on-chip resistor and the frequency tunability using a superconducting quantum interference device. When the two resonators are in resonance, the photons in the high-quality resonator can be efficiently dissipated. We show that the corresponding loaded quality factor can be tuned from above $10^5$ down to a few thousand at 10 GHz in good quantitative agreement with our theoretical model.

cond-mat.mes-hall↗

arXiv2017

Kapitza thermal resistance across individual grain boundaries in graphene

We study heat transport across individual grain boundaries in suspended monolayer graphene using extensive classical molecular dynamics (MD) simulations. We construct bicrystalline graphene samples containing grain boundaries with symmetric tilt angles using the two-dimensional phase field crystal method and then relax the samples with MD. The corresponding Kapitza resistances are then computed using nonequilibrium MD simulations. We find that the Kapitza resistance depends strongly on the tilt angle and shows a clear correlation with the average density of defects in a given grain boundary, but is not strongly correlated with the grain boundary line tension. We also show that quantum effects are significant in quantitative determination of the Kapitza resistance by applying the mode-by-mode quantum correction to the classical MD data. The corrected data are in good agreement with quantum mechanical Landauer-Bütticker calculations.

cond-mat.mes-hall↗

arXiv2017

Bimodal grain-size scaling of thermal transport in polycrystalline graphene from large-scale molecular dynamics simulations

Grain boundaries in graphene are inherent in wafer-scale samples prepared by chemical vapor deposition. They can strongly influence the mechanical properties and electronic and heat transport in graphene. In this work, we employ extensive molecular dynamics simulations to study thermal transport in large suspended polycrystalline graphene samples. Samples of different controlled grain sizes are prepared by a recently developed efficient multiscale approach based on the phase field crystal model. In contrast to previous works, our results show that the scaling of the thermal conductivity with the grain size implies bimodal behaviour with two effective Kapitza lengths. The scaling is dominated by the out-of-plane (flexural) phonons with a Kapitza length that is an order of magnitude larger than that of the in-plane phonons. We also show that in order to get quantitative agreement with the most recent experiments, quantum corrections need to be applied to both the Kapitza conductance of grain boundaries and the thermal conductivity of pristine graphene and the corresponding Kapitza lengths must be renormalized accordingly.

cond-mat.mes-hall↗

arXiv2017

Dynamics of end-pulled polymer translocation through a nanopore

We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory to include friction arising from the trans side subchain. The theory reveals a complicated scenario of multiple scaling regimes depending on the configurations of the cis and the trans side subchains. In the limit of high driving forces $f$ such that the trans subchain is strongly stretched, the theory is in excellent agreement with molecular dynamics simulations and allows an exact analytic solution for the scaling of the translocation time $τ$ as a function of the chain length $N_0$ and $f$. In this regime the asymptotic scaling exponents for $τ \sim N_0^α f^β$ are $α=2$, and $β=-1$. The theory reveals significant correction-to-scaling terms arising from the cis side subchain and pore friction, which lead to a very slow approach to $α=2$ from below as a function of increasing $N_0$.

cond-mat.soft↗

arXiv2017

Multivalent cation induced attraction of anionic polymers by like-charged pores

The efficiency of nanopore-based polymer sensing devices depends on the fast capture of anionic polyelectrolytes by negatively charged pores. This requires the cancellation of the electrostatic barrier associated with repulsive polymer-pore interactions. We develop a correlation-corrected theory to show that the barrier experienced by the polymer can be efficiently overcome by the addition of multivalent cations into the electrolyte solution. Cation adsorption into the pore enhances the screening ability of the pore medium with respect to the bulk reservoir which translates into an attractive force on the polymer. Beyond a critical multivalent cation concentration, this correlation-induced attraction overcomes the electrostatic barrier and triggers the adsorption of the polymer by the like-charged pore. It is shown that like-charge polymer-pore attraction is suppressed by monovalent salt but enhanced by the membrane charge strength and the pore confinement. Our predictions may provide enhanced control over polymer motion in translocation experiments.

cond-mat.soft↗

arXiv2017

Thermal conductivity decomposition in two-dimensional materials: Application to graphene

Two-dimensional materials have unusual phonon structures due to the presence of flexural (out-of-plane) modes. Although molecular dynamics simulations have been extensively used to study heat transport in such materials, conventional formalisms treat the phonon dynamics isotropically. Here, we decompose the microscopic heat current in atomistic simulations into in-plane and out-of-plane components, corresponding to the in-plane and out-of-plane phonon dynamics, respectively. This decomposition allows for direct computation of the corresponding thermal conductivity components in two-dimensional materials. We apply this decomposition to study heat transport in suspended graphene, using both equilibrium and non-equilibrium molecular dynamics simulations. We show that the flexural component is responsible for about two thirds of the total thermal conductivity in unstrained graphene, and the acoustic flexural component is responsible for the logarithmic divergence of the conductivity when a sufficiently large tensile strain is applied.

cond-mat.mes-hall↗

arXiv2017

Controlling Polymer Capture and Translocation by Electrostatic Polymer-Pore Interactions

Polymer translocation experiments typically involve anionic polyelectrolytes such as DNA molecules driven through negatively charged nanopores. Quantitative modelling of polymer capture to the nanopore followed by translocation therefore necessitates the consideration of the electrostatic barrier resulting from like-charge polymer-pore interactions. To this end, in this work we couple mean-field level electrohydrodynamic equations with the Smoluchowski formalism to characterize the interplay between the electrostatic barrier, the electrophoretic drift, and the electro-osmotic liquid flow. In particular, we find that due to distinct ion density regimes where the salt screening of the drift and barrier effects occur, there exists a characteristic salt concentration maximizing the probability of barrier-limited polymer capture into the pore. We also show that in the barrier-dominated regime, the polymer translocation time increases exponentially with the membrane charge and decays exponentially fast with the pore radius and the salt concentration. These results suggest that the alteration of these parameters in the barrier-driven regime can be an efficient way to control the duration of the translocation process and facilitate more accurate measurements of the ionic current signal in the pore.

cond-mat.soft↗

arXiv2017

Plasmonically Enhanced Reflectance of Heat Radiation from Low-Bandgap Semiconductor Microinclusions

Increased reflectance from the inclusion of highly scattering particles at low volume fractions in an insulating dielectric offers a promising way to reduce radiative thermal losses at high temperatures. Here, we investigate plasmonic resonance driven enhanced scattering from microinclusions of low-bandgap semiconductors (InP, Si, Ge, PbS, InAs and Te) in an insulating composite to tailor its infrared reflectance for minimizing thermal losses from radiative transfer. To this end, we compute the spectral properties of the microcomposites using Monte Carlo modeling and compare them with results from Fresnel equations. The role of particle size-dependent Mie scattering and absorption efficiencies, and, scattering anisotropy are studied to identify the optimal microinclusion size and material parameters for maximizing the reflectance of the thermal radiation. For composites with Si and Ge microinclusions we obtain reflectance efficiencies of 57 - 65% for the incident blackbody radiation from sources at temperatures in the range 400 - 1600 °C. Furthermore, we observe a broadbanding of the reflectance spectra from the plasmonic resonances due to charge carriers generated from defect states within the semiconductor bandgap. Our results thus open up the possibility of developing efficient high-temperature thermal insulators through use of the low-bandgap semiconductor microinclusions in insulating dielectrics.

cond-mat.mtrl-sci↗

arXiv2017

Propulsion and controlled steering of magnetic nanohelices

Externally controlled motion of micro and nanomotors in a fluid environment constitutes a promising tool in biosensing, targeted delivery and environmental remediation. In particular, recent experiments have demonstrated that fuel-free propulsion can be achieved through the application of external magnetic fields on magnetic helically shaped structures. The magnetic interaction between helices and the rotating field induces a torque that rotates and propels them via the coupled rotational-translational motion. Recent works have shown that there exist certain optimal geometries of helical shapes for propulsion. However, experiments show that controlled motion remains a challenge at the nanoscale due to Brownian motion that interferes with the deterministic motion and makes it difficult to achieve controlled steering. In the present work we employ quantitatively accurate simulation methodology to design a setup for which magnetic nanohelices of 30 nm in radius, with and without cargo, can be accurately propelled and steered in the presence of thermal fluctuations. In particular, we demonstrate fast transport of such nanomotors and devise protocols in manipulating external fields to achieve directionally controlled steering at biologically relevant temperatures.

physics.flu-dyn↗

arXiv2017

Controlled propulsion and separation of helical particles at the nanoscale

Controlling the motion of nano and microscale objects in a fluid environment is a key factor in designing optimized tiny machines that perform mechanical tasks such as transport of drugs or genetic material in cells, fluid mixing to accelerate chemical reactions, and cargo transport in microfluidic chips. Directed motion is made possible by the coupled translational and rotational motion of asymmetric particles. A current challenge in achieving directed and controlled motion at the nanoscale lies in overcoming random Brownian motion due to thermal fluctuations in the fluid. We use a hybrid lattice-Boltzmann Molecular Dynamics method with full hydrodynamic interactions and thermal fluctuations to demonstrate that controlled propulsion of individual nanohelices in an aqueous environment is possible. We optimize the propulsion velocity and the efficiency of externally driven nanohelices. We quantify the importance of the thermal effects on the directed motion by calculating the Péclet number for various shapes, number of turns and pitch lengths of the helices. Consistent with the experimental microscale separation of chiral objects, our results indicate that in the presence of thermal fluctuations at Péclet numbers $>10$, chiral particles follow the direction of propagation according to its handedness and the direction of the applied torque making separation of chiral particles possible at the nanoscale. Our results provide criteria for the design and control of helical machines at the nanoscale.

physics.flu-dyn↗

arXiv2016

Driven translocation of a semi-flexible polymer through a nanopore

We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory (IFTP), and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length $\tilde{\ell}_p$ the {\it trans} side friction must be explicitly taken into account to properly describe the translocation process. In addition, the scaling of the end-to-end distance $R_N$ as a function of the chain length $N$ must be known. To this end, we first derive a semi-analytic scaling form for $R_N$, which reproduces the limits of a rod, an ideal chain, and an excluded volume chain in the appropriate limits. We then quantitatively characterize the nature of the {\it trans} side friction based on MD simulations of semi-flexible chains. Augmented with these two factors, the modified IFTP theory shows that there are three main regimes for the scaling of the average translocation time $τ\propto N^α$. In the stiff chain (rod) limit $N/\tilde{\ell}_p \ll 1$, {$α= 2$}, which continuously crosses over in the regime $ 1 < N/\tilde{\ell}_p < 4$ towards the ideal chain behavior with {$α= 3/2$}, which is reached in the regime $N/\tilde{\ell}_p \sim 10^2$. Finally, in the limit $N/\tilde{\ell}_p \gg 10^6$ the translocation exponent approaches its symptotic value $1+ν$, where $ν$ is the Flory exponent. Our results are in good agreement with available simulations and experimental data.

cond-mat.soft↗

arXiv2016

Efficient protocol for qubit initialization with a tunable environment

We propose an efficient qubit initialization protocol based on a dissipative environment that can be dynamically adjusted. Here the qubit is coupled to a thermal bath through a tunable harmonic oscillator. On-demand initialization is achieved by sweeping the oscillator rapidly into resonance with the qubit. This resonant coupling with the engineered environment induces fast relaxation to the ground state of the system, and a consecutive rapid sweep back to off resonance guarantees weak excess dissipation during quantum computations. We solve the corresponding quantum dynamics using a Markovian master equation for the reduced density operator of the qubit-bath system. This allows us to optimize the parameters and the initialization protocol for the qubit. Our analytical calculations show that the ground-state occupation of our system is well protected during the fast sweeps of the environmental coupling and, consequently, we obtain an estimate for the duration of our protocol by solving the transition rates between the low-energy eigenstates with the Jacobian diagonalization method. Our results suggest that the current experimental state of the art for the initialization speed of superconducting qubits at a given fidelity can be considerably improved.

cond-mat.mes-hall↗

arXiv2016

Quantifying non-Markovianity due to driving and a finite-size environment in an open quantum system

We study non-Markovian effects present in a driven qubit coupled to a finite environment using a recently proposed model developed in the context of calorimetric measurements of open quantum systems. To quantify the degree of non-Markovianity we use the Breuer-Laine-Piilo (BLP) measure [Breuer \textit{et al.}, Phys. Rev. Lett. \textbf{103}, 210401 (2009)]. We show that information backflow only occurs in the case of driving in which case we investigate the dependence of memory effects on the environment size, driving amplitude and coupling to the environment. We show that the degree of non-Markovianity strongly depends on the ratio between the driving amplitude and the coupling strength. We also show that the degree of non-Markovianity does not decrease monotonically as a function of the environment size.

quant-ph↗

arXiv2016

Comparison between quantum jumps and master equation in the presence of a finite environment

We study the equivalence between the recently proposed finite environment quantum jump model and a master equation approach. We derive microscopically the master equation for a qubit coupled to a finite bosonic environment and show that the master equation is equivalent with the finite environment quantum jump model. We analytically show that both the methods produce the same moments of work when the work is defined through the two-measurement protocol excluding the interaction energy. However, when compared to the work moments computed using the power operator approach, we find a difference in the form of the work moments. To numerically verify our results, we study a qubit coupled to an environment consisting of ten two-level systems.

quant-ph↗