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DOE OSTI2026

Knowledge gaps for neuromorphic ionic computing

BACKGROUND Neuromorphic computing, inspired by the human brain’s ability to process information efficiently, represents a transformative approach to computation. In this Review, we explore the emerging field of neuromorphic ionic computing, which leverages ionic conduction and coupling to mimic neural processes, and identify critical knowledge gaps that must be addressed to realize its full potential. A central theme of the discussion is energy efficiency, a challenge that is both a limitation and an opportunity for this technology. Although complementary metal-oxide semiconductor (CMOS)–based neuromorphic technologies have made strides in scaling to billions of neurons and are increasingly applied in artificial intelligence and numerical computing, they remain orders of magnitude behind the human brain in terms of connectivity and energy efficiency. Neuromorphic ionic computing promises to overcome these limitations by leveraging the distinct architectural and operational principles of the brain. Our brains achieve this energy efficiency by combining several key features: using the same network elements to store and process information; using an incredibly complex and massively interconnected three-dimensional (3D) network of locally active elements that enables sparsity, robustness in the presence of noise, adaptation, and life-long learning; computing at comparatively low voltage and frequency; and last, taking advantage of a plethora of ions and small molecules as information carriers. Here, we propose that ionic computing systems can take advantage of similar features to achieve substantial gains in energy efficiency. ADVANCES Since the first reports of neuromorphic ionic behavior in nanofluidic channels, we have witnessed an explosion of reports that used ionic devices to produce synaptomimetic behaviors. However, achieving the goals of ionic computing requires not only implementation of much more sophisticated device functionality but also overcoming fundamental barriers in materials science, device architecture, and system integration. Current ionic devices, even those incorporating state-of-the-art materials, still suffer from limited functionality and stability, which restrict their performance and increase energy demands. Developing new materials with enhanced ionic properties is essential to overcome these limitations. Similarly, the design of neuromorphic devices must evolve to leverage the particular advantages of ionic processes. Existing architectures often follow a single-information-carrier logic of conventional electronics or are constructed of mesoscale fluidics, failing to capitalize on the energy-efficient mechanisms inherent to ionic systems or implement the multiple-information-carrier paradigm. Current neuromorphic chips focus on large-scale networks of analog memory elements based on mechanisms such as charge trap (flash), filamentary, phase change, or spin, which are built on top of a network of artificial CMOS neurons. Although such prototype networks have achieved impressive performance, it is difficult to envision how they can implement the key features such as massive connectivity, sophisticated plasticity, adaptability, sparsity, and “multichromatic” computing. Although small-scale devices have demonstrated promising results, integrating them, maintaining energy efficiency, and implementing temperature control as systems grow in complexity and size to computationally relevant scale remain major hurdles. Furthermore, interfacing neuromorphic ionic devices with existing computing technologies presents technical and conceptual challenges that will require innovative approaches that combine insights from neuroscience, materials science, and engineering. OUTLOOK Despite these challenges, the potential impact of neuromorphic ionic computing is profound with potential applications ranging from artificial intelligence to robotics and beyond. We also argue that neuromorphic ionic computing systems should not, at least in the beginning, compete with CMOS technologies but rather should focus on applications that require extreme energy efficiency with chemical and/or biological compatibility, such as biomedical applications (for example, brain-computer interfaces), environmental monitoring, and agricultural and food applications. Ultimately, this Review highlights the crucial role of interdisciplinary collaboration in advancing the field. Neuromorphic ionic computing is not merely a technological innovation; it represents a substantial step toward sustainable computation, aligning with the growing demand for energy-conscious solutions in a world that is increasingly reliant on data and computation.

Neuromorphic↗

DOE OSTI2020

Gating of Hydrophobic Nanopores with Large Anions

In this report, understanding ion transport in nanoporous materials is critical to a wide variety of energy and environmental technologies, ranging from ion-selective membranes, drug delivery, and biosensing, to ion batteries and supercapacitors. While nanoscale transport is often described by continuum models that rely on a point charge description for ions and a homogeneous dielectric medium for the solvent, here, we show that transport of aqueous solutions at a hydrophobic interface can be highly dependent on the size and hydration strength of the solvated ions. Specifically, measurements of ion current through single silicon nitride nanopores that contain a hydrophobic-hydrophilic junction show that transport properties are dependent not only on applied voltage but also the type of anion. We find that in Cl - -contained solutions the nanopores only conducted ionic current above a negative voltage threshold. On the other hand, introduction of large polarizable anions, such as Br - and I - , facilitated the pore wetting, making the pore conductive at all examined voltages. Molecular dynamics simulations revealed that the large anions, Br - and I - , have a weaker solvation shell compared to that of Cl - , and consequently were prone to migrate from the aqueous solution to the hydrophobic surface, leading to the anion accumulation responsible for pore wetting. The results are essential for designing nanoporous systems that are selective to ions of the same charge, for realization of ion-induced wetting in hydrophobic pores, as well as for fundamental understanding on the role of ion hydration shell on the properties of solid/liquid interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2013

Conductance of Ion Channels - Theory vs. Experiment

Transmembrane ion channels mediate a number of essential physiological processes in a cell ranging from regulating osmotic pressure to transmission of neural signals. Kinetics and selectivity of ion transport is of critical importance to a cell and, not surprisingly, it is a subject of numerous experimental and theoretical studies. In this presentation we will analyze in detail computer simulations of two simple channels from fungi - antiamoebin and trichotoxin. Each of these channels is made of an alpha-helical bundle of small, nongenomically synthesized peptides containing a number of rare amino acids and exhibits strong antimicrobial activity. We will focus on calculating ionic conductance defined as the ratio of ionic current through the channel to applied voltage. From molecular dynamics simulations, conductance can be calculated in at least two ways, each involving different approximations. Specifically, the current, given as the number of charges transferred through the channel per unit of time, can be obtained from the number of events in which ions cross the channel during the simulation. This method works well for large currents (high conductance values and/or applied voltages). If the number of crossing events is small, reliable estimates of current are difficult to achieve. Alternatively, conductance can be estimated assuming that ion transport can be well approximated as diffusion in the external potential given by the free energy profile. Then, the current can be calculated by solving the one-dimensional diffusion equation in this external potential and applied voltage (the generalized Nernst-Planck equation). To do so three ingredients are needed: the free energy profile, the position-dependent diffusion coefficient and the diffusive flux of ions into the channel. All these quantities can be obtained from molecular dynamics simulations. An important advantage of this method is that it can be used equally well to estimating large and small currents. In addition, once the free energy profile becomes available the full current-voltage dependence can be readily obtained. For both channels we carried out calculations using both approaches. We also tested the main assumptions underlying the diffusive model, such as uncorrelated nature of individual crossing events and Fickian diffusion. The accuracy and consistency of different methods will be discussed. Finally we will discuss how comparisons between calculated and measured ionic conductance and selectivity of transport can be used for determining structural models of the channels.

Pohorille, Andrew↗

DOE OSTI2022

Defect-driven anomalous transport in fast-ion conducting solid electrolytes

We report solid-state ionic conduction is a key enabler of electrochemical energy storage and conversion. The mechanistic connections between material processing, defect chemistry, transport dynamics, and practical performance are of considerable importance, but remain incomplete. Here, inspired by studies of fluids and biophysical systems, we re-examine anomalous diffusion in the iconic two-dimensional fast-ion conductors, the β- and β"-aluminas. Using large-scale simulations, we reproduce the frequency dependence of alternating-current ionic conductivity data. We show how the distribution of charge-compensating defects, modulated by processing, drives static and dynamic disorder, which lead to persistent sub-diffusive ion transport at macroscopic timescales. We deconvolute the effects of repulsions between mobile ions, the attraction between the mobile ions and charge-compensating defects, and geometric crowding on ionic conductivity. Our quantitative framework based on these model solid electrolytes connects their atomistic defect chemistry to macroscopic performance with minimal assumptions and enables mechanism-driven 'atoms-to-device' optimization of fast-ion conductors.

25 ENERGY STORAGE↗

DOE OSTI2020

Dynamic Structure and Phase Behavior of a Block Copolymer Electrolyte under dc Polarization

There is an important consideration when designing lithium battery electrolytes for advanced applications is how the electrolyte facilitates ion transport at fast charge and discharge rates. Large current densities are accompanied by large salt concentration gradients across the electrolyte. Nanostructured composite electrolytes have been proposed to enable the use of high energy density lithium metal anodes, but many questions about the interplay between the electrolyte morphology and the salt concentration gradient that forms under dc polarization remain unanswered. To address these questions, we use an in situ small-angle X-ray scattering technique to examine the nanostructure of a polystyrene- block -poly(ethylene oxide) copolymer electrolyte under dc polarization with spatial and temporal resolution. In the quiescent state, the electrolyte exhibits a lamellar morphology. The passage of ionic current in a lithium symmetric cell leads to the formation of concurrent phases: a disordered morphology near the negative electrode, lamellae in the center of the cell, and coexisting lamellae and gyroid near the positive electrode. The most surprising result of this study was obtained after the applied electric field was turned off: a current-induced gyroid phase grows in volume for 6 h in spite of the absence of an obvious driving force. We show that this reflects the formation of localized pockets of salt-dense electrolyte, termed concentration hotspots, under dc polarization. Our methods may be applied to understand the dynamic structure of composite electrolytes at appreciable current densities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2003

Detection of Strand Cleavage And Oxidation Damage Using Model DNA Molecules Captured in a Nanoscale Pore

We use a biological nano-scale pore to distinguish among individual DNA hairpins that differ by a single site of oxidation or a nick in the sugar-phosphate backbone. In earlier work we showed that the protein ion channel alpha-hemolysin can be used as a detector to distinguish single-stranded from double-stranded DNA, single base pair and single nucleotide differences. This resolution is in part a result of sensitivity to structural changes that influence the molecular dynamics of nucleotides within DNA. The strand cleavage products we examined here included a 5-base-pair (5-bp) hairpin with a 5-prime five-nucleotide overhang, and a complementary five-nucleotide oligomer. These produced predictable shoulder-spike and rapid near-full blockade signatures, respectively. When combined, strand annealing was monitored in real time. The residual current level dropped to a lower discrete level in the shoulder-spike blockade signatures, and the duration lengthened. However, these blockade signatures had a shorter duration than the unmodified l0bp hairpin. To test the pore sensitivity to nucleotide oxidation, we examined a 9-bp hairpin with a terminal 8-oxo-deoxyguanosine (8-oxo-dG), or a penultimate 8-oxo-dG. Each produced blockade signatures that differed from the otherwise identical control 9bp hairpins. This study showed that DNA structure is modified sufficiently by strand cleavage or oxidation damage at a single site to alter in a predictable manner the ionic current blockade signatures produced. This technique improves the ability to assess damage to DNA, and can provide a simple means to help characterize the risks of radiation exposure. It may also provide a method to test radiation protection.

Vercoutere, W.↗

DOE OSTI2026

Heterogeneous Multilayer Nanopores via Chemically Tuned Dielectric Breakdown for Single‐Molecule Sensing

Solid-state nanopores are powerful platforms for single-molecule sensing, yet their performance is often constrained by fabrication complexity, noise, and limited control over surface properties. Here we report a direct method to fabricate heterogeneous multilayer nanopores using chemically tuned controlled dielectric breakdown (CT-CDB). We integrate hBN, MoS 2 , or graphene atop a silicon nitride membrane to form five distinct bilayer and tri-layer architectures, with bare SiN x nanopore as a control. CT-CDB achieves pore formation reproducibly through material-stacks with high efficiency, good pore size control, and strong yield, validated by various characterizations. Transferrin protein translocation experiments, supported by simulations, reveal that multilayer configurations modulate protein conformations, ionic current blockade and dwell time distributions, reflecting combined effects of membrane type, interfacial chemistry, and local electric field gradients. A supervised machine learning framework is implemented to assist identifying multilayer structure effects embedded in signal signatures, with over 96% accuracy. This work presents a modular and scalable framework for functional nanopore engineering with complex structural integration, thereby expanding the potential of 2D materials in single-molecule sensing applications.

2D materials↗

DOE OSTI2021

Bipolar Membranes for Ion Management in (Photo)Electrochemical Energy Conversion

Conspectus (Photo)electrochemical energy conversion is important in the development of a carbon-neutral energy economy because it can provide a pathway for mitigating the intermittency of renewable energy sources such as wind and solar. In order to operate efficiently, these technologies, which include photoelectrochemical cells, water and CO 2 electrolyzers, fuel cells, and redox flow batteries, require fast charge transfer kinetics at the electrode/electrolyte interface as well as robust ion management in the electrolyte. In conventional electrolyzers and fuel cells, the electrolyte is strongly acidic or basic and ionic current is carried by H + or OH – ions. In contrast, photoelectrodes and electrocatalysts for water splitting are often studied in buffered solutions. The question of ion balance in these systems led us to analyze the polarization losses due to ion concentration gradients in cells that employed various buffer–membrane combinations. Continuously driving the buffer ions across an ionomer membrane not only lowers the buffer capacity of an aqueous electrolyte but also introduces pH gradients that result in significant energy losses. To address the problem, we and other groups have studied the use of reverse-biased bipolar membranes (BPMs) in (photo)electrolytic cells. BPMs consist of an anion exchange layer (AEL) laminated with a cation exchange layer (CEL) and are usually equipped with a catalytic layer in between to accelerate the water dissociation reaction. At the AEL/CEL interface, water dissociates into protons and hydroxide ions, which replenish those consumed at the cathode and anode. Compared to conventional water electrolyzers with proton/anion exchange membranes (PEM/AEM), BPM electrolyzers provide the unique advantage of continuously operating the cathode and anode under different pH conditions, which is desirable when the two electrode reactions have different pH requirements. BPMs also enable the use of buffered electrolytes at pH values that are optimized for electrode stability and product selectivity in applications such as CO 2 electrolysis. Product crossover losses and CO 2 pumping can be dramatically reduced in BPM-based CO 2 electrolyzers, relative to conventional alkaline membranes, by electrostatic repulsion (of anionic products) and electroosmotic drag (for neutral products). BPM-based gas fed CO 2 electrolyzers can achieve high current density, but they suffer from low Faradaic efficiency (FE) due to the acidic local environment of the CEL. This problem can be mitigated by adding an aqueous buffering layer or by creating a weak acid cation exchange film on the CEL face of the membrane. The use of BPMs in fuel cells and redox flow batteries offers some interesting advantages. Configurations with both reverse and forward bias have been studied, but forward bias has been favored due to material compatibility, reaction kinetics, and thermodynamic considerations. The net reaction at the AEL/CEL interface is the acid–base neutralization reaction, which has a high inherent reaction rate constant, but in the BPM is limited to a nanometric space-charge layer and requires efficient catalysis to achieve high current density. Understanding the mechanism of the acid–base neutralization and the opposite process, the water dissociation reaction, will be essential for improving the performance of forward-biased BPMs. In conclusion, this Account reviews our current understanding of the working mechanisms of BPMs and discusses how we can use them to effectively manage ions for various (photo)electrochemical applications.

Yan, Zhifei↗

DOE OSTI2021

Improving Thermal Stability of Perovskite Solar Cells by Suppressing Ion Migration Using Copolymer Grain Encapsulation

Thermal stability of organic–inorganic hybrid perovskites (OIHPs) remains as one of the critical challenges against the stable operation of perovskite solar cells (PSCs) in direct sunlight with elevated temperatures. Here, we show that the addition of a polystyrene-co-polyacrylonitrile (SAN) copolymer can significantly enhance thermal stability of OIHPs and improve the stability of the corresponding PSCs by suppressing the migration of organic cations in OHIP. The methylammonium lead iodide (MAPI) with SAN incorporated within the perovskite layer featured a superior thermal stability compared to pure MAPI without SAN, only displaying an average of 5–15% decrease in PCE even after continuous thermal aging for 24 h at 100 °C. The secondary ion mass spectrometry revealed that the thermal degradation of the pure MAPI was largely associated with MA+ out-migration. Conducting atomic force microscopy analysis further indicated that the incorporated SAN led to a suppression of ionic currents present at the grain boundaries of the perovskite film, which was understood by high immiscibility between SAN and MA+ components as confirmed by the experimentally estimated Flory–Huggins parameter between them. This study newly identifies a potential of using polymer grain encapsulation for enhancing thermal stability of OIHPs and their solar cell performance by suppressing the out-diffusion of cationic organic components.

36 MATERIALS SCIENCE↗

DOE OSTI2026

A nanoporous capacitive electrochemical ratchet for continuous ion separations

Directed ion transport in liquid electrolyte solutions underlies many phenomena in natural and industrial settings. While nature has evolved structures that drive continuous ion flow without Faradaic redox reactions, establishing this process in synthetic systems has been challenging. Here, in this study, we report an ion pump that drives aqueous ions against a force using a capacitive ratchet mechanism independent of redox reactions. Modulation of an electric potential between thin metallic layers on either face of a nanoporous alumina wafer immersed in solution results in persistent voltages and ionic currents. This occurs due to the nonlinear capacitive nature of electric double layers, whose repeated charging and discharging sustains a continuous ion flux. Using this approach, we demonstrate ratchet-driven electrodialysis that reaches a 50% decrease in the conductivity of the solution in a dilution cell. These ratchet-based ion pumps can enable continuous desalination and selective ion separation using an electrically powered device with no moving parts.

Kautz, Rylan [University of California, Irvine, CA↗

DOE OSTI2025

Unraveling membrane electrode assembly design for electrochemical conversion of carbon dioxide to formate/formic acid

This work presents a one-dimensional continuum modeling approach to investigate various cell architectures used for electrochemical conversion of CO 2 to formate/formic acid. Ion transport is simulated by a system of generalized modified Poisson–Nernst–Planck (GMPNP) equations that reflect the reactive transport phenomena including steric effects as the electrolyte solutions become concentrated. In the cathode catalyst layer, ionic current contributions from both the supporting electrolyte and solid-state ionomer are considered. Voltage and CO 2 utilization breakdowns are utilized to deconvolute the impacts of the cell architecture. The origins of (bi)carbonate formation in the cathode are explored, as the subsequent decrease in CO 2 availability is a key reason for low faradaic efficiencies to formate/formic acid. In addition, the role of a supporting electrolyte (KOH) is investigated to understand its tradeoffs: while the K + ions can improve both conductivity and electrochemically active surface area in the cathode, the presence of OH − ions raises the pH and leads to deleterious formation of (bi)carbonates. To this end, we also present parametric studies on the concentration and flow rate of supplied KOH to the cell, to establish a path towards eliminating the need for a supporting electrolyte.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Peripheral Nerve Magnetoneurography With Optically Pumped Magnetometers

Electrodiagnosis is routinely integrated into clinical neurophysiology practice for peripheral nerve disease diagnoses, such as neuropathy, demyelinating disorders, nerve entrapment/impingement, plexopathy, or radiculopathy. Measured with conventional surface electrodes, the propagation of peripheral nerve action potentials along a nerve is the result of ionic current flow which, according to Ampere’s Law, generates a small magnetic field that is also detected as an “action current” by magnetometers, such as superconducting quantum interference device (SQUID) Magnetoencephalography (MEG) systems. Optically pumped magnetometers (OPMs) are an emerging class of quantum magnetic sensors with a demonstrated sensitivity at the 1 fT/√Hz level, capable of cortical action current detection. But OPMs were ostensibly constrained to low bandwidth therefore precluding their use in peripheral nerve electrodiagnosis. With careful OPM bandwidth characterization, we hypothesized OPMs may also detect compound action current signatures consistent with both Sensory Nerve Action Potential (SNAP) and the Hoffmann Reflex (H-Reflex). In as much, our work confirms OPMs enabled with expanded bandwidth can detect the magnetic signature of both the SNAP and H-Reflex. Taken together, OPMs now show potential as an emerging electrodiagnostic tool.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Chemical Sensing and Chemoresponsive Pumping with Conical-Pore Polymeric Membranes

Synthetic membranes containing asymmetrically shaped pores have been shown to rectify the ionic current flowing through the membrane. Ion-current rectification means that such membranes produce nonlinear current–voltage curves analogous to those observed with solid-state diode rectifiers. In order to observe this ion-current rectification phenomenon, the asymmetrically shaped pores must have pore-wall surface charge. Pore-wall surface charge also allows for electroosmotic flow (EOF) to occur through the membrane. We have shown that, because ion-current is rectified, EOF is likewise rectified in such membranes. This means that flow through the membrane depends on the polarity of the voltage applied across the membrane, one polarity producing a higher, and the opposite producing a lower, flow rate. As is reviewed here, these ion-current and EOF rectification phenomena are being used to develop new sensing technologies. Results obtained from an ion-current-based sensor for hydrophobic cations are reviewed. In addition, ion-current and EOF rectification can be combined to make a new type of device—a chemoresponsive nanofluidic pump. This is a pump that either turns flow on or turns flow off, when a specific chemical species is detected. Results from a prototype Pb 2+ chemoresponsive pump are also reviewed here.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2001

LabHEART: an interactive computer model of rabbit ventricular myocyte ion channels and Ca transport

An interactive computer program, LabHEART, was developed to simulate the action potential (AP), ionic currents, and Ca handling mechanisms in a rabbit ventricular myocyte. User-oriented, its design allows switching between voltage and current clamp and easy on-line manipulation of key parameters to change the original formulation. The model reproduces normal rabbit ventricular myocyte currents, Ca transients, and APs. We also changed parameters to simulate data from heart failure (HF) myocytes, including reduced transient outward (I(to)) and inward rectifying K currents (I(K1)), enhanced Na/Ca exchange expression, and reduced sarcoplasmic reticulum Ca-ATPase function, but unaltered Ca current density. These changes caused reduced Ca transient amplitude and increased AP duration (especially at lower frequency) as observed experimentally. The model shows that the increased Na/Ca exchange current (I(NaCa)) in HF lowers the intracellular [Ca] threshold for a triggered AP from 800 to 540 nM. Similarly, the decrease in I(K1) reduces the threshold to 600 nM. Changes in I(to) have no effect. Combining enhanced Na/Ca exchange with reduced I(K1) (as in HF) lowers the threshold to trigger an AP to 380 nM. These changes reproduce experimental results in HF, where the contributions of different factors are not readily distinguishable. We conclude that the triggered APs that contribute to nonreentrant ventricular tachycardia in HF are due approximately equally (and nearly additively) to alterations in I(NaCa) and I(K1). A free copy of this software can be obtained at http://www.meddean.luc.edu/lumen/DeptWebs/physio/bers.html.

NASA Discipline Cardiopulmonary↗

NASA NTRS1996

Characterization of individual polynucleotide molecules using a membrane channel

We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. The passage of each molecule is detected as a transient decrease of ionic current whose duration is proportional to polymer length. Channel blockades can therefore be used to measure polynucleotide length. With further improvements, the method could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA.

NASA Discipline Exobiology↗

NASA NTRS2013

Properties and Performance Attributes of Novel Co-extruded Polyolefin Battery Separator Materials: Electrical Properties - Part 2

As NASA prepares for its next era of manned spaceflight missions, advanced energy storage technologies are being developed and evaluated to address and enhance future mission needs and technical requirements. Cell-level components for advanced lithium-ion batteries possessing higher energy, more reliable performance and enhanced, inherent safety characteristics have been under development within the NASA infrastructure. A key component for safe and reliable cell performance is the cell separator, which separates the two energetic electrodes and functions to inhibit the occurrence of an internal short circuit but preserves an ionic current. Recently, a new generation of co-extruded separator films has been developed by ExxonMobil Chemical and introduced into their battery separator product portfolio. Several grades of this new separator material were evaluated with respect to dynamic mechanical properties and safety-related performance attributes, and the results of these evaluations were previously reported in "Part 1: Mechanical Properties" of this publication. This current paper presents safety-related performance results for these novel materials obtained by employing a complementary experimental methodology, which involved the analysis of separator impedance characteristics as a function of temperature. The experimental results from this study are discussed with respect to potential cell safety enhancement for future aerospace as well as for terrestrial energy storage needs, and they are compared with pertinent mechanical properties of these materials, as well as with current state-of-the practice separator materials.

Baldwin, Richard S.↗

NASA NTRS2015

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗

NASA NTRS2017

Abiotic Synthesis of Nucleic Acids: Hypochromicity and Future Research

The earliest forms of life would likely have a protocellular form, with a membrane encapsulating some form of linear charged polymer. These polymers could have enzymatic as well as genetic properties. We can simulate plausible prebiotic conditions in the laboratory to test hypotheses related to this concept. In earlier work we have shown that mononucleotides organized within a multilamellar lipid matrix can produce oligomers in the anhydrous phase of dehydration- rehydration cycles (Rajamani, 2008). If mononucleotides are in solution at millimolar concentrations, then oligomers resembling RNA are synthesized and exist in a steady state with their monomers DeGuzman, 2014). We have used conventional and novel techniques to demonstrate that secondary structures stabilized by hydrogen bonds may be present in the condensation products produced in dehydration- rehydration cycles that simulate hydrothermal fields that were present on the early Earth. Gel electrophoresis data corroborates the presence of up to 200-base pair length RNA fragments in products of Hydration-Dehydration experiments. Furthermore, hypochromicity measurements demonstrate a degree of hypochromicity found in single RNA strand of known sequence, as well as results that indicate this is true also for a sample of complementary strands of RNA. Analysis of ionic current signatures of known RNA hairpin molecule as measured using a nanopore detector indicate a significant variability in pattern, different from the signatures produced by DNA hairpin molecules. This informs how we may interpret nanopore data gathered from prebiotic simulations.

Glass, K.↗