scholarly journals Modeling the Device Behavior of Biological and Synthetic Nanopores with Reduced Models

Entropy ◽  
2020 ◽  
Vol 22 (11) ◽  
pp. 1259
Author(s):  
Dezső Boda ◽  
Mónika Valiskó ◽  
Dirk Gillespie
Keyword(s):  
Ion Channels ◽  
Degrees Of Freedom ◽  
Ionic Currents ◽  
Response Functions ◽  
Reduced Models ◽  
Rules Of Thumb ◽  
Transport Of Ions ◽  
Current Rectification ◽  
The Right ◽  
Axial Concentration

Biological ion channels and synthetic nanopores are responsible for passive transport of ions through a membrane between two compartments. Modeling these ionic currents is especially amenable to reduced models because the device functions of these pores, the relation of input parameters (e.g., applied voltage, bath concentrations) and output parameters (e.g., current, rectification, selectivity), are well defined. Reduced models focus on the physics that produces the device functions (i.e., the physics of how inputs become outputs) rather than the atomic/molecular-scale physics inside the pore. Here, we propose four rules of thumb for constructing good reduced models of ion channels and nanopores. They are about (1) the importance of the axial concentration profiles, (2) the importance of the pore charges, (3) choosing the right explicit degrees of freedom, and (4) creating the proper response functions. We provide examples for how each rule of thumb helps in creating a reduced model of device behavior.

scholarly journals An Experimental and Numerical Study of Polyelectrolyte Hydrogel Ionic Diodes: Towards Electrical Detection of Charged Biomolecules

Sensors ◽  
2021 ◽  
Vol 21 (24) ◽  
pp. 8279
Author(s):  
Chenwei Xiong ◽  
Boyin Zhang ◽  
Rong Zhang ◽  
Yifan Liu
Keyword(s):  
Numerical Simulation ◽  
Numerical Study ◽  
Ionic Current ◽  
Ionic Currents ◽  
Microfluidic Chips ◽  
Electrical Detection ◽  
Heterogeneous Distribution ◽  
Transport Of Ions ◽  
Current Rectification ◽  
Polyelectrolyte Hydrogel

Polyelectrolyte hydrogel ionic diodes (PHIDs) have recently emerged as a unique set of iontronic devices. Such diodes are built on microfluidic chips that feature polyelectrolyte hydrogel junctions and rectify ionic currents owing to the heterogeneous distribution and transport of ions across the junctions. In this paper, we provide the first account of a study on the ion transport behavior of PHIDs through an experimental investigation and numerical simulation. The effects of bulk ionic strength and hydrogel pore confinement are experimentally investigated. The ionic current rectification (ICR) exhibits saturation in a micromolar regime and responds to hydrogel pore size, which is subsequently verified in a simulation. Furthermore, we experimentally show that the rectification is sensitive to the dose of immobilized DNA with an exhibited sensitivity of 1 ng/μL. We anticipate our findings would be beneficial to the design of PHID-based biosensors for electrical detection of charged biomolecules.

scholarly journals Slow scrambling in extremal BTZ and microstate geometries

2021 ◽  
Vol 2021 (3) ◽  
Author(s):  
Ben Craps ◽  
Marine De Clerck ◽  
Philip Hacker ◽  
Kévin Nguyen ◽  
Charles Rabideau
Keyword(s):  
Field Theory ◽  
Black Holes ◽  
Degrees Of Freedom ◽  
Average Power ◽  
Nonzero Temperature ◽  
Time Intervals ◽  
Conformal Field ◽  
Btz Black Holes ◽  
The Right ◽  
Extremal Black Holes

Abstract Out-of-time-order correlators (OTOCs) that capture maximally chaotic properties of a black hole are determined by scattering processes near the horizon. This prompts the question to what extent OTOCs display chaotic behaviour in horizonless microstate geometries. This question is complicated by the fact that Lyapunov growth of OTOCs requires nonzero temperature, whereas constructions of microstate geometries have been mostly restricted to extremal black holes.In this paper, we compute OTOCs for a class of extremal black holes, namely maximally rotating BTZ black holes, and show that on average they display “slow scrambling”, characterized by cubic (rather than exponential) growth. Superposed on this average power-law growth is a sawtooth pattern, whose steep parts correspond to brief periods of Lyapunov growth associated to the nonzero temperature of the right-moving degrees of freedom in a dual conformal field theory.Next we study the extent to which these OTOCs are modified in certain “superstrata”, horizonless microstate geometries corresponding to these black holes. Rather than an infinite throat ending on a horizon, these geometries have a very deep but finite throat ending in a cap. We find that the superstrata display the same slow scrambling as maximally rotating BTZ black holes, except that for large enough time intervals the growth of the OTOC is cut off by effects related to the cap region, some of which we evaluate explicitly.

scholarly journals Transcriptomic uniqueness and commonality of the ion channels and transporters in the four heart chambers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sanda Iacobas ◽  
Bogdan Amuzescu ◽  
Dumitru A. Iacobas
Keyword(s):  
Ion Channels ◽  
Cycle Phase ◽  
Functional Roles ◽  
Expression Control ◽  
Gene Expression Control ◽  
Left And Right ◽  
The Right ◽  
Phase Out ◽  
Right Atria ◽  
Agilent Microarrays

AbstractMyocardium transcriptomes of left and right atria and ventricles from four adult male C57Bl/6j mice were profiled with Agilent microarrays to identify the differences responsible for the distinct functional roles of the four heart chambers. Female mice were not investigated owing to their transcriptome dependence on the estrous cycle phase. Out of the quantified 16,886 unigenes, 15.76% on the left side and 16.5% on the right side exhibited differential expression between the atrium and the ventricle, while 5.8% of genes were differently expressed between the two atria and only 1.2% between the two ventricles. The study revealed also chamber differences in gene expression control and coordination. We analyzed ion channels and transporters, and genes within the cardiac muscle contraction, oxidative phosphorylation, glycolysis/gluconeogenesis, calcium and adrenergic signaling pathways. Interestingly, while expression of Ank2 oscillates in phase with all 27 quantified binding partners in the left ventricle, the percentage of in-phase oscillating partners of Ank2 is 15% and 37% in the left and right atria and 74% in the right ventricle. The analysis indicated high interventricular synchrony of the ion channels expressions and the substantially lower synchrony between the two atria and between the atrium and the ventricle from the same side.

Interstitial Nucleus of Cajal Encodes Three-Dimensional Head Orientations in Fick-Like Coordinates

2007 ◽  
Vol 97 (1) ◽  
pp. 604-617 ◽  
Author(s):  
Eliana M. Klier ◽  
Hongying Wang ◽  
J. Douglas Crawford
Keyword(s):  
Coordinate System ◽  
Degrees Of Freedom ◽  
Three Dimensional ◽  
Semicircular Canals ◽  
Head Rotation ◽  
Head Orientation ◽  
Interstitial Nucleus Of Cajal ◽  
The Gaze ◽  
Behavioral Constraints ◽  
The Right

Two central, related questions in motor control are 1) how the brain represents movement directions of various effectors like the eyes and head and 2) how it constrains their redundant degrees of freedom. The interstitial nucleus of Cajal (INC) integrates velocity commands from the gaze control system into position signals for three-dimensional eye and head posture. It has been shown that the right INC encodes clockwise (CW)-up and CW-down eye and head components, whereas the left INC encodes counterclockwise (CCW)-up and CCW-down components, similar to the sensitivity directions of the vertical semicircular canals. For the eyes, these canal-like coordinates align with Listing’s plane (a behavioral strategy limiting torsion about the gaze axis). By analogy, we predicted that the INC also encodes head orientation in canal-like coordinates, but instead, aligned with the coordinate axes for the Fick strategy (which constrains head torsion). Unilateral stimulation (50 μA, 300 Hz, 200 ms) evoked CW head rotations from the right INC and CCW rotations from the left INC, with variable vertical components. The observed axes of head rotation were consistent with a canal-like coordinate system. Moreover, as predicted, these axes remained fixed in the head, rotating with initial head orientation like the horizontal and torsional axes of a Fick coordinate system. This suggests that the head is ordinarily constrained to zero torsion in Fick coordinates by equally activating CW/CCW populations of neurons in the right/left INC. These data support a simple mechanism for controlling head orientation through the alignment of brain stem neural coordinates with natural behavioral constraints.

scholarly journals Ionic bases for electrical remodeling of the canine cardiac ventricle

2013 ◽  
Vol 305 (3) ◽  
pp. H410-H419 ◽  
Author(s):  
Darwin Jeyaraj ◽  
Xiaoping Wan ◽  
Eckhard Ficker ◽  
Julian E. Stelzer ◽  
Isabelle Deschenes ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Phase 1 ◽  
Myocardial Strain ◽  
Ionic Currents ◽  
Left Ventricular ◽  
Electrical Remodeling ◽  
Cardiac Ventricle ◽  
Ionic Mechanisms ◽  
Ventricular Electrical Remodeling

Emerging evidence suggests that ventricular electrical remodeling (VER) is triggered by regional myocardial strain via mechanoelectrical feedback mechanisms; however, the ionic mechanisms underlying strain-induced VER are poorly understood. To determine its ionic basis, VER induced by altered electrical activation in dogs undergoing left ventricular pacing ( n = 6) were compared with unpaced controls ( n = 4). Action potential (AP) durations (APDs), ionic currents, and Ca2+ transients were measured from canine epicardial myocytes isolated from early-activated (low strain) and late-activated (high strain) left ventricular regions. VER in the early-activated region was characterized by minimal APD prolongation, but marked attenuation of the AP phase 1 notch attributed to reduced transient outward K+ current. In contrast, VER in the late-activated region was characterized by significant APD prolongation. Despite marked APD prolongation, there was surprisingly minimal change in ion channel densities but a twofold increase in diastolic Ca2+. Computer simulations demonstrated that changes in sarcolemmal ion channel density could only account for attenuation of the AP notch observed in the early-activated region but failed to account for APD remodeling in the late-activated region. Furthermore, these simulations identified that cytosolic Ca2+ accounted for APD prolongation in the late-activated region by enhancing forward-mode Na+/Ca2+ exchanger activity, corroborated by increased Na+/Ca2+ exchanger protein expression. Finally, assessment of skinned fibers after VER identified altered myofilament Ca2+ sensitivity in late-activated regions to be associated with increased diastolic levels of Ca2+. In conclusion, we identified two distinct ionic mechanisms that underlie VER: 1) strain-independent changes in early-activated regions due to remodeling of sarcolemmal ion channels with no changes in Ca2+ handling and 2) a novel and unexpected mechanism for strain-induced VER in late-activated regions in the canine arising from remodeling of sarcomeric Ca2+ handling rather than sarcolemmal ion channels.

Updating of Finite Element Models Based on a Double Condensation Procedure Using Frequency Response Functions Data

1995 ◽  
Author(s):  
Rémi Berriet ◽  
René Fillod ◽  
Noureddine Bouhaddi
Keyword(s):  
Frequency Response ◽  
Degrees Of Freedom ◽  
Noise Pollution ◽  
Test Case ◽  
Response Functions ◽  
Frequency Response Functions ◽  
Measured Frequency ◽  
Modal Damping ◽  
Applied Forces ◽  
Definition Of

Abstract In order to take into account information from test data, not only at the resonances, but also in the other parts of the measured frequency spectrum, it is of interest to use directly measured Frequency Response Functions (FRF) instead of modal data. We also avoid by this way an experimental modal analysis. In return we have to introduce damping terms into the analytical model, we have to weight the FRF data in a systematic manner and to compute simultaneously a large amount of data. The presented procedure analyses overall these three aspects: definition of modal damping parameters, definition of weighted FRF data and condensation of the problem. This last notion is particularly pointed out. The condensation is performed in two steps : a static condensation of the model on the degrees of freedom corresponding to the location of the sensors, and a simultaneous condensation of experimental and analytical FRF data by a common transformation matrix. The first applications are performed on a simulated test case with large stiffness, mass and modal damping perturbations introduced in the initial model as well as strong noise pollution of measured responses and applied forces.

An appropriate biomechanical model of seated human subjects exposed to whole-body vibration

2021 ◽  
pp. 146441932110394
Author(s):  
Raj Desai ◽  
Anirban Guha ◽  
Pasumarthy Seshu
Keyword(s):  
Degrees Of Freedom ◽  
Human Subjects ◽  
Computational Cost ◽  
Biomechanical Model ◽  
Whole Body ◽  
Body Parts ◽  
Lumped Parameter ◽  
Long Duration ◽  
The One ◽  
The Right

Long duration automobile-induced vibration is the cause of many ailments to humans. Predicting and mitigating these vibrations through seat requires a good model of seated human body. A good model is the one that strikes the right balance between modelling difficulty and simulation results accuracy. Increasing the number of body parts which have been separately modelled and increasing the number of ways these parts are connected to each other increase the number of degrees of freedom of the entire model. A number of such models have been reported in the literature. These range from simple lumped parameter models with limited accuracy to advanced models with high computational cost. However, a systematic comparison of these models has not been reported till date. This work creates eight such models ranging from 8 to 26 degrees of freedom and tries to identify the model which strikes the right balance between modelling complexity and results accuracy. A comparison of the models’ prediction with experimental data published in the literature allows the identification of a 12 degree of freedom backrest supported model as optimum for modelling complexity and prediction accuracy.

Ion Channel Permeation and Selectivity

2019 ◽  
Author(s):  
Juan J. Nogueira ◽  
Ben Corry
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Ion Selectivity ◽  
Ionic Currents ◽  
Biological Processes ◽  
Ion Permeation ◽  
Voltage Gated ◽  
Physical Mechanisms ◽  
Theoretical Approaches ◽  
Mechanistic Insight

Many biological processes essential for life rely on the transport of specific ions at specific times across cell membranes. Such exquisite control of ionic currents, which is regulated by protein ion channels, is fundamental for the proper functioning of the cells. It is not surprising, therefore, that the mechanism of ion permeation and selectivity in ion channels has been extensively investigated by means of experimental and theoretical approaches. These studies have provided great mechanistic insight but have also raised new questions that are still unresolved. This chapter first summarizes the main techniques that have provided significant knowledge about ion permeation and selectivity. It then discusses the physical mechanisms leading to ion permeation and the explanations that have been proposed for ion selectivity in voltage-gated potassium, sodium, and calcium channels.

MADYMO Simulations of Occupant and Vehicle Kinematics in Offset and Oblique Barrier Tests

2005 ◽  
Author(s):  
Rex T. Shea ◽  
Jiri Kral
Keyword(s):  
Degrees Of Freedom ◽  
Three Dimensional ◽  
Vertical Direction ◽  
Oblique Impact ◽  
Test Method ◽  
Vehicle Interior ◽  
Center Of Rotation ◽  
Frontal Impacts ◽  
Coordinate Origin ◽  
The Right

Oblique and offset impacts occur more frequently than full frontal impacts and the resulting occupant and vehicle kinematics are more complicated. Simulations of these test modes are more involved with added vehicle degrees of freedom. Additional occupant interactions with the vehicle interior need to be considered so that the occupant kinematics can be correlated more accurately. In order to capture the vehicle motion in an offset or oblique impact, a prescribed motion approach is preferred where the vehicle is given a three-dimensional motion with six degrees of freedom. With a planar motion assumption, the dominant angular motion about the vertical direction can be derived from linear accelerations measured at two locations where the vehicle deformation is a minimum. In a previous study the angular kinematics was given to a coordinate origin located on the vehicle centerline and longitudinally near the rear rocker. The instantaneous center of rotation was assumed to be fixed at this point during the event. This is referred to as Method I in this paper. A new approach, referred to as Method II, applied translational displacement to three bodies, which carried the passenger compartment through stiff spring elements. The displacements were integrated from measured accelerations, eliminating the uncertainty of a shifting center of rotation. Both methods assumed the vehicle frame between the front and rear rockers as a rigid body. The IP and steering column intrusions and floor deformations were neglected. The results from both methods were correlated to a pair of 40 kph 30 degree angle impact tests and an IIHS ODB test. Method II showed a slightly better timing correlation for the angle tests and the IIHS ODB test. However, both methods didn’t predict the lateral head contact for the driver in the left angle test and the passenger in the right angle test. More interior details have to be included in the model to capture the lateral motion of the occupants. The prescribed motion method is a more general approach than the commonly used inverse kinematics method, and can be applied to full frontal impact as well. The versatility of the method provides a basis for a modular approach in occupant simulations.

scholarly journals ELECTROMAGNETIC DUALITY ON THE LIGHT-FRONT IN THE PRESENCE OF EXTERNAL SOURCES

2000 ◽  
Vol 15 (30) ◽  
pp. 4739-4748 ◽  
Author(s):  
ASMITA MUKHERJEE ◽  
SOMDATTA BHATTACHARYA
Keyword(s):  
Degrees Of Freedom ◽  
Transverse Field ◽  
Light Front ◽  
Duality Transformation ◽  
Hamiltonian Density ◽  
Free Theory ◽  
External Sources ◽  
Normal Light ◽  
The Right ◽  
Dynamical Field

We investigate the issue of electromagnetic duality on the light-front. We work with Zwanziger's theory of electric and magnetic sources which is appropriate for treating duality. When quantized on the light-front in the light-front gauge, this theory yields two independent phase space degrees of freedom, namely the two transverse field components, the right number to describe the gauge field sector of normal light-front QED and also the appropriate commutator between them. The electromagnetic duality transformation formulated in terms of them is similar in form to the Susskind transformation proposed for the free theory, provided one identifies them as the dynamical field components of the photon on the light-front in the presence of magnetic sources. The Hamiltonian density written in terms of these components is invariant under the duality transformation.

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