In this paper, we present a computational model to describe the electrical response of a constricted graphene nanoribbon (GNR) to biomolecules translocating through a nanopore. For this purpose, we use a self-consistent 3D Poisson equation solver coupled with an accurate three-orbital tight-binding model to assess the ability for a gate electrode to modulate both the carrier concentration as well as the conductance in the GNR. We also investigate the role of electrolytic screening on the sensitivity of the conductance to external charges and find that the gate electrode can either suppress or enhance the screening of biomolecular charges in the nanopore depending on the value of its potential. Translocating a double-stranded DNA molecule along the pore axis imparted a large change in the conductance at particular gate voltages, suggesting that such a device can be used to sense translocating biomolecules and can be actively tuned to maximize its sensitivity.

Local modulation of temperature has emerged as a new mechanism for regulation of molecular transport through nanopores. Predicting the effect of such modulations on nanopore transport requires simulation protocols capable of reproducing non-uniform temperature gradients observed in experiment. Conventional molecular dynamics (MD) method typically employs a single thermostat for maintaining a uniform distribution of temperature in the entire simulation domain, and, therefore, can not model local temperature variations. In this article, we describe a set of simulation protocols that enable modeling of nanopore systems featuring non-uniform distributions of temperature. First, we describe a method to impose a temperature gradient in all-atom MD simulations based on a boundary-driven non-equilibrium MD protocol. Then, we use this method to study the effect of temperature gradient on the distribution of ions in bulk solution (the thermophoretic effect). We show that DNA nucleotides exhibit differential response to the same temperature gradient. Next, we describe a method to directly compute the effective force of a thermal gradient on a prototypical biomolecule-a fragment of double-stranded DNA. Following that, we demonstrate an all-atom MD protocol for modeling thermophoretic effects in solid-state nanopores. We show that local heating of a nanopore volume can be used to regulate the nanopore ionic current. Finally, we show how continuum calculations can be coupled to a coarse-grained model of DNA to study the effect of local temperature modulation on electrophoretic motion of DNA through plasmonic nanopores. The computational methods described in this article are expected to find applications in rational design of temperature-responsive nanopore systems.

Ion channels are part of nature's solution for regulating biological environments. Every ion channel consists of a chain of amino acids carrying a strong and sharply varying permanent charge, folded in such a way that it creates a nanoscopic aqueous pore spanning the otherwise mostly impermeable membranes of biological cells. These naturally occurring proteins are particularly interesting to device engineers seeking to understand how such nanoscale systems realize device-like functions. Availability of high-resolution structural information from X-ray crystallography, as well as large-scale computational resources, makes it possible to conduct realistic ion channel simulations. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator, offers a powerful and general approach to study ion channel permeation. BioMOCA is based on the Boltzmann Transport Monte Carlo (BTMC) and Particle-Particle-Particle-Mesh (P(3)M) methodologies developed at the University of Illinois at Urbana-Champaign. In this paper we briefly discuss the various approaches to simulating ion flow in channel systems that are currently being pursued by the biophysics and engineering communities, and present the effect of having anisotropic dielectric constants on ion flow through a number of nanopores with different effective diameters.

The present work establishes a unique framework for the simulation study of ion-motive pumps in general and the Na(+)/K(+)-ATPase, or sodium pump, in particular. We shall discuss the implications of electrostatic analysis, valence calculations, and protein cavity data, each carried over data extracted from molecular dynamics simulations, on the structure-function relationship of Na(+)/K(+)-ATPase. These diverse set of tools will be used to investigate atomic-level characteristics that remain undetermined such as ion binding and accessibility.

We outline the basic operational, structural and functional features of ion motive ATPases: transmembrane proteins central to biological functions of all animal cells. As an example we discuss the modeling problems associated with the operation of the surface membrane Na(+),K(+)-ATPase and skeletal muscle sarcoplasmic reticulum Ca(2+)-ATPase and focus on the frameworks required for their solution. There are three basic problems: identification of the pathway for ion permeation, prediction of ion binding rate coefficients and affinities based on the structure of the protein, and prediction of conformational changes of protein structure and the associated movement of charges within the membrane dielectric. A solution strategy useful in approaching the first two problems and preliminary results obtained using molecular dynamics simulations are also presented.

The electronic structure and dielectric screening of finite-length armchair carbon nanotubes are studied with both tight-binding and ab initio methods. Good agreement is found in the band gap oscillation patterns and dielectric constants, which validates the tight-binding method as a reliable and fast approach to describe the screening effect of carbon nanotubes. For an illustration, our method is applied to a system consisting of a short (6,6) nanotube filled with six water molecules. Substantial screening of the water dipoles through the nanotube is observed. This polarization effect should have an important influence on the permeation of water and other biomolecules inside carbon nanotubes.

The Boltzmann transport equation is commonly considered to be the best semi-classical description of carrier transport in semiconductors, providing precise information about the distribution of carriers with respect to time (one dimension), location (three dimensions), and momentum (three dimensions). However, numerical solutions for the seven-dimensional carrier distribution functions are very demanding. The most common solution approach is the stochastic Monte Carlo method, because the gigabytes of memory requirements of deterministic direct solution approaches has not been available until recently. As a remedy, the higher accuracy provided by solutions of the Boltzmann transport equation is often exchanged for lower computational expense by using simpler models based on macroscopic quantities such as carrier density and mean carrier velocity. Recent developments for the deterministic spherical harmonics expansion method have reduced the computational cost for solving the Boltzmann transport equation, enabling the computation of carrier distribution functions even for spatially three-dimensional device simulations within minutes to hours. We summarize recent progress for the spherical harmonics expansion method and show that small currents, reasonable execution times, and rare events such as low-frequency noise, which are all hard or even impossible to simulate with the established Monte Carlo method, can be handled in a straight-forward manner. The applicability of the method for important practical applications is demonstrated for noise simulation, small-signal analysis, hot-carrier degradation, and avalanche breakdown.

Simulation of total ionizing dose effects in field isolation of FET technologies requires transport mechanisms in the oxide to be considered. In this work, carrier transport and trapping in thick oxides using the finite elements method in the Synopsys Sentaurus platform are systematically simulated. Carriers are generated in the oxide and are transported out through a direct contact with the gate and thermionic emission to the silicon. The method is applied to calibrate experimental results of 400 nm capacitors irradiated at total doses of 11.6 kRad ( ) and 58 kRad ( ). Drift-diffusion-enabled trapping as well as other issues that arise from the involved physics are discussed. Effective bulk trap densities and activation energies of the traps are extracted.

The semiconductor industry is currently challenged by the emergence of Internet of Things, Big data, and deep-learning techniques to enable object recognition and inference in portable computers. These revolutions demand new technologies for memory and computation going beyond the standard CMOS-based platform. In this scenario, resistive switching memory (RRAM) is extremely promising in the frame of storage technology, memory devices, and in-memory computing circuits, such as memristive logic or neuromorphic machines. To serve as enabling technology for these new fields, however, there is still a lack of industrial tools to predict the device behavior under certain operation schemes and to allow for optimization of the device properties based on materials and stack engineering. This work provides an overview of modeling approaches for RRAM simulation, at the level of technology computer aided design and high-level compact models for circuit simulations. Finite element method modeling, kinetic Monte Carlo models, and physics-based analytical models will be reviewed. The adaptation of modeling schemes to various RRAM concepts, such as filamentary switching and interface switching, will be discussed. Finally, application cases of compact modeling to simulate simple RRAM circuits for computing will be shown.

We propose and investigate a biosensor based on a transparent dielectric-modulated dual-trench gate-engineered metal-oxide-semiconductor field-effect transistor (DM DT GE-MOSFET) for label-free detection of biomolecules with enhanced sensitivity and efficiency. Various sensing parameters such as the / ratio and the threshold voltage shift are evaluated as metrics to validate the proposed sensing device. Additionally, (the sensitivity) is also analyzed, considering both positively and negatively charged biomolecules. In addition, radiofrequency (RF) sensing parameters such as the transconductance gain and the cutoff frequency are taken into account to provide further insight into the sensitivity of the proposed device. Furthermore, the linearity, distortion, and noise immunity of the device are evaluated to confirm the overall performance of the biosensor at high (GHz) frequency. The results indicate that the proposed biosensor exhibits a value of 0.68 for positively charged biomolecules at a very low drain bias of 0.2 V. The proposed device can thus be used as an alternative to conventional FET-based biosensors.

Entangled quantum particles, in which operating on one particle instantaneously influences the state of the entangled particle, are attractive options for carrying quantum information at the nanoscale. However, fully-describing entanglement in traditional time-dependent quantum transport simulation approaches requires significant computational effort, bordering on being prohibitive. Considering electrons, one approach to analyzing their entanglement is through modeling the Coulomb interaction via the Wigner formalism. In this work, we reduce the computational complexity of the time evolution of two interacting electrons by resorting to reasonable approximations. In particular, we replace the Wigner potential of the electron-electron interaction by a local electrostatic field, which is introduced through the spectral decomposition of the potential. It is demonstrated that for some particular configurations of an electron-electron system, the introduced approximations are feasible. Purity, identified as the maximal coherence for a quantum state, is also analyzed and its corresponding analysis demonstrates that the entanglement due to the Coulomb interaction is well accounted for by the introduced local approximation.

Plasmonic structures may improve cell performance in a variety of ways. More accurate determining of the optical influence, unlike ideal simulations, requires modeling closer to experimental cases. In this modeling and simulation, irregular nanostructures were chosen and divided into three groups and some modes. For each mode, different sizes of nanoparticles were randomly selected, which could result in pre-determined average particle size and standard deviation. By 3D finite-difference time-domain (3D-FDTD), the optical plasmonic properties of that mode in a solar cell structure were investigated when the nanostructure was added to the buffer/active layer of the organic solar cell. The far- and near-field results were used to compare the plasmonic behavior, relying on the material and geometry. By detailed simulations, Al and Ag nanostructure at the interface of the ZnO/active layer can improve organic solar cell performance optically, especially by the near-field effect. Unlike Au and relative Ag, the Al nanostructured sample showed less parasitic absorption loss.

Realizing the promises of molecular electronic devices requires an understanding of transport on the nanoscale. Here, we consider a Su-Schrieffer-Heeger model for semi-conducting trans-polyacetylene molecular wires in which we endow charge carriers with a finite lifetime. The aim of this exercise is two-fold: (i) the simplicity of the model allows an insightful numerical and analytical comparison of the Landauer and Kubo linear-response formalism; (ii) we distill the prototypical characteristics of charge transport through gapped mesoscopic systems and compare these to bulk semiconductors. We find that both techniques yield a residual differential conductance at low temperatures for contacted polyacetylene chains of arbitrary length-in line with the resistivity saturation in some correlated narrow-gap semiconductors. Quantitative agreement, however, is limited to not too long molecules. Indeed, while the Landauer transmission is suppressed exponentially with the system size, the Kubo response only decays hyperbolically. Our findings inform the choice of transport methodologies for the ab initio modelling of molecular devices.

NanoTCAD ViDES (Versatile DEvice Simulator) is an open-source suite of computing codes aimed at assessing the operation and the performance of nanoelectronic devices. It has served the computational nanoelectronic community for almost two decades and it is freely available to researchers around the world in its website (http://vides.nanotcad.com), being employed in hundreds of works by many electronic device simulation groups worldwide. We revise the code structure and its main modules and we present the new features directed towards (i) multi-scale approaches exploiting ab-initio electron-structure calculations, aiming at the exploitation of new physics in electronic devices, (ii) the inclusion of arbitrary heterostructures of layered materials to devise original device architectures and operation, and (iii) the exploration of novel low-cost, green technologies in the mesoscopic scale, as, e.g. printed electronics.