James Fonseca | Purdue University (original) (raw)

Papers by James Fonseca

Journal of Computational Electronics, 2016

The goal of this project is to improve the simulation of an electrical device known as a Resonant... more The goal of this project is to improve the simulation of an electrical device known as a Resonant Tunneling Diode (RTD). Diodes are in most electronic devices today, but RTDs have 10 times greater switching speeds than regular diodes. This increase in efficiency would have impacts from supercomputers to the next big cell phone. The increased functionality of the simulation tool will come from implementing more recent mathematical solvers and modeling techniques. The simulation tool makes use of a variant of Non-Equilibrium Green Functions (NEGF) with an effective mass approximation. The two contacts are treated as equilibrium regions and the channel as a non-equilibrium region. The tool is capable of simulating multi-barrier devices and allows for significant user input. The output is being developed to allow the user to see the results of bias sweeps as well as side-by-side graphs of conduction band edge, transmission probability, energy resolved current and current-voltage characteristics. Upon completion of the tool it will become available through nanoHUB, a scientific and engineering gateway providing interactive online resources. This will allow for the broad impact in classrooms, laboratories, and industries around the world. RTDs will become significantly more important as our electronics continue to grow in power and shrink in size. The simulation tool will continue to be updated with future advancements in technology.

Biophys J, 2009

A simple pillbox model with two adjustable parameters accounts for the selectivity of both DEEA C... more A simple pillbox model with two adjustable parameters accounts for the selectivity of both DEEA Ca channels and DEKA Na channels in many ionic solutions of different composition and concentration. Only the side chains are different in the model of the Ca and Na channels. Parameters are the same for both channels in all solutions. 'Pauling' radii are used for ions. No information from crystal structures is used in the model. Side chains are grossly approximated as spheres. The predicted properties of the Na and Ca channels are very different. How can such a simple model give such powerful results when chemical intuition says that selectivity depends on the precise relation of ions and side chains? We use Monte Carlo simulations of this model that determine the most stable-lowest free energy-structure of the ions and side chains. Structure is the computed consequence of the forces in this model. The relationship of ions and side chains vary with ionic solution and are very different in simulations of the Na and Ca channels. Selectivity is a consequence of the 'induced fit' of side chains to ions and depends on the flexibility (entropy) of the side chains as well as their location. The model captures the relation of side chains and ions well enough to account for selectivity of both Na channels and Ca channels in the wide range of conditions measured in experiments. Evidently, the structures in the real Na and Ca channels responsible for selectivity are self-organized, at their free energy minimum. Oversimplified models are enough to account for selectivity if the models calculate the 'most stable' structure as it changes from solution to solution, and mutation to mutation.

A detailed theoretical study of the optical absorption in self-assembled quantum dots is presente... more A detailed theoretical study of the optical absorption in self-assembled quantum dots is presented in this paper. A rigorous atomistic strain model as well as a sophisticated electronic band structure model are used to ensure accurate prediction of the optical transitions in these devices . The optimized models presented in this paper are able to reproduce the experimental results with an error less than 1$\%$. The effects of incident light polarization, alloy mole fraction, quantum dot dimensions, and doping have been investigated. The in-plane polarized light absorption is more significant than the perpendicularly polarized light absorption. Increasing the mole fraction of the strain controlling layer leads to a lower energy gap and larger absorption wavelength. Surprisingly, the absorption wavelength is highly sensitive to changes in the dot diameter, but almost insensitive to changes in the dot height. This unpredicted behavior is explained by sensitivity analysis of different factors which affect the optical transition energy.

2015 International Workshop on Computational Electronics (IWCE), 2015

Journal of computational electronics, 2005

We outline the basic operational, structural and functional features of ion motive ATPases: trans... more 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.

ABSTRACT The interface roughness is a crucial factor in DG-MOSFET performance, as indicated by th... more ABSTRACT The interface roughness is a crucial factor in DG-MOSFET performance, as indicated by the International Technology Roadmap for semiconductors. A modified nanoMOS simulator is employed based on the non-equilibrium Green's function (NEGF) to model DG-MOSFETs with rough interfaces. Reconstruction of rough interfaces with accurate spectral models is based on a 1D Fourier synthesis.

14th IEEE International Conference on Nanotechnology, 2014

2012 15th International Workshop on Computational Electronics, IWCE 2012, 2012

Abstract Archimedes is the GNU package for Monte Carlo (MC) semiconductor devices simulations. Si... more Abstract Archimedes is the GNU package for Monte Carlo (MC) semiconductor devices simulations. Since its very first release in 2005, users have been able to download the source code under the GNU Public License (GPL). Since then, many features have been introduced in this package, including the ability to perform Archimedes simulation on nanoHUB. org. This paper presents the current code status and anticipated developments.

Solid-State Electronics, 2004

In the sub-50-nm scale, the aggressive scaling of MOSFETs is expected to culminate in dual-gate (... more In the sub-50-nm scale, the aggressive scaling of MOSFETs is expected to culminate in dual-gate (DG) architectures on SOI substrates. DG MOSFETs are widely accepted to be the ultimate design that silicon can deliver in terms of on and off currents. So far, the design efforts on these novel structures have concentrated on ideal geometries and doping profiles. However, at nanometer scale, devices fabricated with lithography and etching techniques cannot deliver perfect reproductions of the ideal design and suffer significantly from fluctuation effects associated with random doping and interfaces. While the former is less important in undoped, thin-body architecture, the interface roughness is a crucial factor in DG MOSFET performance, as indicated by the International Technology Roadmap for Semiconductors.

Journal of Membrane Biology, 2007

Palytoxin (PTX) opens a pathway for ions to pass through Na,K-ATPase. We investigate here whether... more Palytoxin (PTX) opens a pathway for ions to pass through Na,K-ATPase. We investigate here whether PTX also acts on non-

Discrete and Continuous Dynamical Systems - Series B, 2012

We introduce a mathematical model, which describes the charge inversion phenomena in systems with... more We introduce a mathematical model, which describes the charge inversion phenomena in systems with a charged wall or boundary. This model may prove helpful in understanding semiconductor devices, ion channels, and electrochemical systems like batteries that depend on complex distributions of charge for their function. The mathematical model is derived using the energy variational approach that takes into account ion diffusion, electrostatics, finite size effects, and specific boundary behavior. In ion dynamic theory, a well-known system of equations is the Poisson-Nernst-Planck (PNP) equation that includes entropic and electrostatic energy. The PNP type of equation can also be derived by the energy variational approach. However, the PNP equations have not produced the charge inversion/layering in charged wall situations presumably because the conventional PNP does not include the finite size of ions and other physical features needed to create the charge inversion. In this paper, we investigate the key features needed to produce the charge inversion phenomena using a mathematical model, the energy variational approach. One of the key features is a finite size (finite volume) effect, which is an unavoidable property of ions important for their dynamics on small scales. The other is an interfacial constraint to capture the spatial variation of electroneutrality in systems with charged walls. The interfacial constraint is established by the diffusive interface approach that approximately describes the boundary effect produced by the charged wall. The energy variational approach gives us a mathematically self-consistent way to introduce the interfacial constraint. We mainly discuss those two key features in this paper. Employing the energy variational approach, we derive a non-local partial differential equation with a total energy consisting of the entropic energy, electrostatic energy, repulsion energy representing the excluded volume effect, and the contribution of an interfacial constraint related to overall electroneutrality between bulk/bath and wall. The resulting mathematical model produces the charge inversion phenomena near charged walls. We compare the computational results of the mathematical model to those of Monte-Carlo computations. 1 of cement . The complex distributions are closely related to distributions in and near proteins and lipid membranes .

Biophysical Journal, 2011

Biophysical Journal, 2009

agreement with published FRET data. Cross-correlation matrices revealed correlated motions betwee... more agreement with published FRET data. Cross-correlation matrices revealed correlated motions between the A and phosphorylation (P) domains in both E1 and E2 states. In contrast, anticorrelated motions were observed between N and A/P domains, with slight differences between E1 and E2, suggesting a Ca 2þ effect. Solvent-accessible surface area around the ATP site increased in the simulated E2 state. Conclusions: (a) Crystal structures of E1 and E2 states of SERCA are not representative of the populations under physiological conditions, where the two structures differ much less than in the crystal. (b) The simulation indicates a much more accessible ATP-binding site than observed in the E2 crystal structure. (c) Calcium-induced modulation of interdomain anticorrelated motions involving the N domain may be important for ATP binding, catalysis and gating. Electrochromic styryl dyes are in use now for almost two decades to detect ion movements in various P-type ATPases. The extremely hydrophobic dye molecules have a high partition coefficient in favor of the hydrophobic core of lipid phase of membrane preparations. Fluorescence changes are obtained by modification of local electric fields in the membrane dielectric produced by ions bound to or released from binding sites of the ion pumps. To obtain significant signals a prerequisite is a high density of active proteins in the membranes. This limitation could be overcome by solubilization of the Na,K-ATPase in mixed micelles of protein/lipid/detergent obtained by incubation of microsomal membranes from rabbit kidney with dodecyl maltoside. In this preparation the specific enzyme activity of the Na,K-ATPase was reduced compared to that in native membranes. This effect was assigned to the highly affected lipid environment of the singularized proteins which may be depleted of specific lipid components and the content of dodecyl maltoside. The fluorescence changes which were detected with the styryl dye RH421 showed smaller amplitudes than in the case of purified membrane preparations, however, the responses on Na þ binding, Na þ release upon enzyme phosphorylation and conformation transition, and subsequent K þ binding in the E 2 P conformation were clearly detectable. Na þ binding affinity and its dependence on Mg 2þ concentration and buffer pH, as well as K þ affinity were comparable to the results obtained with native preparations. The transfer of the method to solubilized ion pumps will allow investigations of mutants isolated from cell in which they were expressed in low density. In addition, this approach will possibly extend method also to the investigation of ion channel molecules by electrochromic styryl dyes.

Biophysical Journal, 2009

The role of flexibility in the selectivity of calcium channels is studied using a simple model wi... more The role of flexibility in the selectivity of calcium channels is studied using a simple model with two parameters that accounts for the selectivity of calcium (and sodium) channels in many ionic solutions of different compositions and concentrations using two parameters with unchanging values. We compare the distribution of side chains (oxygens) and cations (Na + and Ca 2+ ) and integrated quantities. We compare the occupancies of cations Ca 2+ /Na + and linearized conductance of Na + . The distributions show a strong dependence on the locations of fixed side chains and the flexibility of the side chains. Holding the side chains fixed at certain predetermined locations in the selectivity filter distorts the distribution of Ca 2+ and Na + in the selectivity filter. However, integrated quantities-occupancy and normalized conductance-are much less sensitive. Our results show that some flexibility of side chains is necessary to avoid obstruction of the ionic pathway by oxygen ions in 'unfortunate' fixed positions. When oxygen ions are mobile, they adjust 'automatically' and move 'out of the way', so they can accommodate the permeable cations in the selectivity filter. Structure is the computed consequence of the forces in this model. The structures are self-organized, at their free energy minimum. The relationship of ions and side chains varies with an ionic solution. Monte Carlo simulations are particularly well suited to compute induced-fit, self-organized structures because the simulations yield an ensemble of structures near their free energy minimum. The exact location and mobility of oxygen ions has little effect on the selectivity behavior of calcium channels. Seemingly, nature has chosen a robust mechanism to control selectivity in calcium channels: the first-order determinant of selectivity is the density of charge in the selectivity filter. The density is determined by filter volume along with the charge and excluded volume of structural ions confined within it. Flexibility seems a second-order determinant. These results justify our original assumption that the important factor in Ca 2+ versus Na + selectivity is the density of oxygen ions in the selectivity filter along with (charge) polarization (i.e. dielectric properties). The assumption of maximum mobility of oxygens seems to be an excellent approximate working hypothesis in the absence of exact structural information. These conclusions, of course, apply to what we study here. Flexibility and fine structural details may have an important role in other properties of calcium channels that are not studied in this paper. They surely have important roles in other channels, enzymes, and proteins.

Biophysical Journal, 2010

Journal of Computational Electronics, 2013

As semiconductor devices scale to new dimensions, the materials and designs become more dependent... more As semiconductor devices scale to new dimensions, the materials and designs become more dependent on atomic details. NEMO5 is a nanoelectronics modeling package designed for comprehending the critical multi-scale, multi-physics phenomena through efficient computational approaches and quantitatively modeling new generations of nanoelectronic devices as well as predicting novel device architectures and phenomena. This article seeks to provide updates on the current status of the tool and new functionality, including advances in quantum transport simulations and with materials such as metals, topological insulators, and piezoelectrics.

Abstract—The miniaturization of semiconductor devices has reached the point where the number of a... more Abstract—The miniaturization of semiconductor devices has reached the point where the number of atoms is countable and geometries are formed in three dimensions. The Nanoelectronic Modeling tool suite NEMO5 is designed to comprehend the critical multi-scale, multi-physics phenomena and deliver results to engineers, scientists, and students through efficient computational approaches. Keywords: Atomistic Simulations; Nanoelectronic; Tightbinding; NEGF; Multiphysics; Multiscale; Parallel Computing.

Journal of Computational Electronics, 2016

The goal of this project is to improve the simulation of an electrical device known as a Resonant... more The goal of this project is to improve the simulation of an electrical device known as a Resonant Tunneling Diode (RTD). Diodes are in most electronic devices today, but RTDs have 10 times greater switching speeds than regular diodes. This increase in efficiency would have impacts from supercomputers to the next big cell phone. The increased functionality of the simulation tool will come from implementing more recent mathematical solvers and modeling techniques. The simulation tool makes use of a variant of Non-Equilibrium Green Functions (NEGF) with an effective mass approximation. The two contacts are treated as equilibrium regions and the channel as a non-equilibrium region. The tool is capable of simulating multi-barrier devices and allows for significant user input. The output is being developed to allow the user to see the results of bias sweeps as well as side-by-side graphs of conduction band edge, transmission probability, energy resolved current and current-voltage characteristics. Upon completion of the tool it will become available through nanoHUB, a scientific and engineering gateway providing interactive online resources. This will allow for the broad impact in classrooms, laboratories, and industries around the world. RTDs will become significantly more important as our electronics continue to grow in power and shrink in size. The simulation tool will continue to be updated with future advancements in technology.

Biophys J, 2009

A simple pillbox model with two adjustable parameters accounts for the selectivity of both DEEA C... more A simple pillbox model with two adjustable parameters accounts for the selectivity of both DEEA Ca channels and DEKA Na channels in many ionic solutions of different composition and concentration. Only the side chains are different in the model of the Ca and Na channels. Parameters are the same for both channels in all solutions. 'Pauling' radii are used for ions. No information from crystal structures is used in the model. Side chains are grossly approximated as spheres. The predicted properties of the Na and Ca channels are very different. How can such a simple model give such powerful results when chemical intuition says that selectivity depends on the precise relation of ions and side chains? We use Monte Carlo simulations of this model that determine the most stable-lowest free energy-structure of the ions and side chains. Structure is the computed consequence of the forces in this model. The relationship of ions and side chains vary with ionic solution and are very different in simulations of the Na and Ca channels. Selectivity is a consequence of the 'induced fit' of side chains to ions and depends on the flexibility (entropy) of the side chains as well as their location. The model captures the relation of side chains and ions well enough to account for selectivity of both Na channels and Ca channels in the wide range of conditions measured in experiments. Evidently, the structures in the real Na and Ca channels responsible for selectivity are self-organized, at their free energy minimum. Oversimplified models are enough to account for selectivity if the models calculate the 'most stable' structure as it changes from solution to solution, and mutation to mutation.

A detailed theoretical study of the optical absorption in self-assembled quantum dots is presente... more A detailed theoretical study of the optical absorption in self-assembled quantum dots is presented in this paper. A rigorous atomistic strain model as well as a sophisticated electronic band structure model are used to ensure accurate prediction of the optical transitions in these devices . The optimized models presented in this paper are able to reproduce the experimental results with an error less than 1$\%$. The effects of incident light polarization, alloy mole fraction, quantum dot dimensions, and doping have been investigated. The in-plane polarized light absorption is more significant than the perpendicularly polarized light absorption. Increasing the mole fraction of the strain controlling layer leads to a lower energy gap and larger absorption wavelength. Surprisingly, the absorption wavelength is highly sensitive to changes in the dot diameter, but almost insensitive to changes in the dot height. This unpredicted behavior is explained by sensitivity analysis of different factors which affect the optical transition energy.

2015 International Workshop on Computational Electronics (IWCE), 2015

Journal of computational electronics, 2005

We outline the basic operational, structural and functional features of ion motive ATPases: trans... more 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.

ABSTRACT The interface roughness is a crucial factor in DG-MOSFET performance, as indicated by th... more ABSTRACT The interface roughness is a crucial factor in DG-MOSFET performance, as indicated by the International Technology Roadmap for semiconductors. A modified nanoMOS simulator is employed based on the non-equilibrium Green's function (NEGF) to model DG-MOSFETs with rough interfaces. Reconstruction of rough interfaces with accurate spectral models is based on a 1D Fourier synthesis.

14th IEEE International Conference on Nanotechnology, 2014

2012 15th International Workshop on Computational Electronics, IWCE 2012, 2012

Abstract Archimedes is the GNU package for Monte Carlo (MC) semiconductor devices simulations. Si... more Abstract Archimedes is the GNU package for Monte Carlo (MC) semiconductor devices simulations. Since its very first release in 2005, users have been able to download the source code under the GNU Public License (GPL). Since then, many features have been introduced in this package, including the ability to perform Archimedes simulation on nanoHUB. org. This paper presents the current code status and anticipated developments.

Solid-State Electronics, 2004

In the sub-50-nm scale, the aggressive scaling of MOSFETs is expected to culminate in dual-gate (... more In the sub-50-nm scale, the aggressive scaling of MOSFETs is expected to culminate in dual-gate (DG) architectures on SOI substrates. DG MOSFETs are widely accepted to be the ultimate design that silicon can deliver in terms of on and off currents. So far, the design efforts on these novel structures have concentrated on ideal geometries and doping profiles. However, at nanometer scale, devices fabricated with lithography and etching techniques cannot deliver perfect reproductions of the ideal design and suffer significantly from fluctuation effects associated with random doping and interfaces. While the former is less important in undoped, thin-body architecture, the interface roughness is a crucial factor in DG MOSFET performance, as indicated by the International Technology Roadmap for Semiconductors.

Journal of Membrane Biology, 2007

Palytoxin (PTX) opens a pathway for ions to pass through Na,K-ATPase. We investigate here whether... more Palytoxin (PTX) opens a pathway for ions to pass through Na,K-ATPase. We investigate here whether PTX also acts on non-

Discrete and Continuous Dynamical Systems - Series B, 2012

We introduce a mathematical model, which describes the charge inversion phenomena in systems with... more We introduce a mathematical model, which describes the charge inversion phenomena in systems with a charged wall or boundary. This model may prove helpful in understanding semiconductor devices, ion channels, and electrochemical systems like batteries that depend on complex distributions of charge for their function. The mathematical model is derived using the energy variational approach that takes into account ion diffusion, electrostatics, finite size effects, and specific boundary behavior. In ion dynamic theory, a well-known system of equations is the Poisson-Nernst-Planck (PNP) equation that includes entropic and electrostatic energy. The PNP type of equation can also be derived by the energy variational approach. However, the PNP equations have not produced the charge inversion/layering in charged wall situations presumably because the conventional PNP does not include the finite size of ions and other physical features needed to create the charge inversion. In this paper, we investigate the key features needed to produce the charge inversion phenomena using a mathematical model, the energy variational approach. One of the key features is a finite size (finite volume) effect, which is an unavoidable property of ions important for their dynamics on small scales. The other is an interfacial constraint to capture the spatial variation of electroneutrality in systems with charged walls. The interfacial constraint is established by the diffusive interface approach that approximately describes the boundary effect produced by the charged wall. The energy variational approach gives us a mathematically self-consistent way to introduce the interfacial constraint. We mainly discuss those two key features in this paper. Employing the energy variational approach, we derive a non-local partial differential equation with a total energy consisting of the entropic energy, electrostatic energy, repulsion energy representing the excluded volume effect, and the contribution of an interfacial constraint related to overall electroneutrality between bulk/bath and wall. The resulting mathematical model produces the charge inversion phenomena near charged walls. We compare the computational results of the mathematical model to those of Monte-Carlo computations. 1 of cement . The complex distributions are closely related to distributions in and near proteins and lipid membranes .

Biophysical Journal, 2011

Biophysical Journal, 2009

agreement with published FRET data. Cross-correlation matrices revealed correlated motions betwee... more agreement with published FRET data. Cross-correlation matrices revealed correlated motions between the A and phosphorylation (P) domains in both E1 and E2 states. In contrast, anticorrelated motions were observed between N and A/P domains, with slight differences between E1 and E2, suggesting a Ca 2þ effect. Solvent-accessible surface area around the ATP site increased in the simulated E2 state. Conclusions: (a) Crystal structures of E1 and E2 states of SERCA are not representative of the populations under physiological conditions, where the two structures differ much less than in the crystal. (b) The simulation indicates a much more accessible ATP-binding site than observed in the E2 crystal structure. (c) Calcium-induced modulation of interdomain anticorrelated motions involving the N domain may be important for ATP binding, catalysis and gating. Electrochromic styryl dyes are in use now for almost two decades to detect ion movements in various P-type ATPases. The extremely hydrophobic dye molecules have a high partition coefficient in favor of the hydrophobic core of lipid phase of membrane preparations. Fluorescence changes are obtained by modification of local electric fields in the membrane dielectric produced by ions bound to or released from binding sites of the ion pumps. To obtain significant signals a prerequisite is a high density of active proteins in the membranes. This limitation could be overcome by solubilization of the Na,K-ATPase in mixed micelles of protein/lipid/detergent obtained by incubation of microsomal membranes from rabbit kidney with dodecyl maltoside. In this preparation the specific enzyme activity of the Na,K-ATPase was reduced compared to that in native membranes. This effect was assigned to the highly affected lipid environment of the singularized proteins which may be depleted of specific lipid components and the content of dodecyl maltoside. The fluorescence changes which were detected with the styryl dye RH421 showed smaller amplitudes than in the case of purified membrane preparations, however, the responses on Na þ binding, Na þ release upon enzyme phosphorylation and conformation transition, and subsequent K þ binding in the E 2 P conformation were clearly detectable. Na þ binding affinity and its dependence on Mg 2þ concentration and buffer pH, as well as K þ affinity were comparable to the results obtained with native preparations. The transfer of the method to solubilized ion pumps will allow investigations of mutants isolated from cell in which they were expressed in low density. In addition, this approach will possibly extend method also to the investigation of ion channel molecules by electrochromic styryl dyes.

Biophysical Journal, 2009

The role of flexibility in the selectivity of calcium channels is studied using a simple model wi... more The role of flexibility in the selectivity of calcium channels is studied using a simple model with two parameters that accounts for the selectivity of calcium (and sodium) channels in many ionic solutions of different compositions and concentrations using two parameters with unchanging values. We compare the distribution of side chains (oxygens) and cations (Na + and Ca 2+ ) and integrated quantities. We compare the occupancies of cations Ca 2+ /Na + and linearized conductance of Na + . The distributions show a strong dependence on the locations of fixed side chains and the flexibility of the side chains. Holding the side chains fixed at certain predetermined locations in the selectivity filter distorts the distribution of Ca 2+ and Na + in the selectivity filter. However, integrated quantities-occupancy and normalized conductance-are much less sensitive. Our results show that some flexibility of side chains is necessary to avoid obstruction of the ionic pathway by oxygen ions in 'unfortunate' fixed positions. When oxygen ions are mobile, they adjust 'automatically' and move 'out of the way', so they can accommodate the permeable cations in the selectivity filter. Structure is the computed consequence of the forces in this model. The structures are self-organized, at their free energy minimum. The relationship of ions and side chains varies with an ionic solution. Monte Carlo simulations are particularly well suited to compute induced-fit, self-organized structures because the simulations yield an ensemble of structures near their free energy minimum. The exact location and mobility of oxygen ions has little effect on the selectivity behavior of calcium channels. Seemingly, nature has chosen a robust mechanism to control selectivity in calcium channels: the first-order determinant of selectivity is the density of charge in the selectivity filter. The density is determined by filter volume along with the charge and excluded volume of structural ions confined within it. Flexibility seems a second-order determinant. These results justify our original assumption that the important factor in Ca 2+ versus Na + selectivity is the density of oxygen ions in the selectivity filter along with (charge) polarization (i.e. dielectric properties). The assumption of maximum mobility of oxygens seems to be an excellent approximate working hypothesis in the absence of exact structural information. These conclusions, of course, apply to what we study here. Flexibility and fine structural details may have an important role in other properties of calcium channels that are not studied in this paper. They surely have important roles in other channels, enzymes, and proteins.

Biophysical Journal, 2010

Journal of Computational Electronics, 2013

As semiconductor devices scale to new dimensions, the materials and designs become more dependent... more As semiconductor devices scale to new dimensions, the materials and designs become more dependent on atomic details. NEMO5 is a nanoelectronics modeling package designed for comprehending the critical multi-scale, multi-physics phenomena through efficient computational approaches and quantitatively modeling new generations of nanoelectronic devices as well as predicting novel device architectures and phenomena. This article seeks to provide updates on the current status of the tool and new functionality, including advances in quantum transport simulations and with materials such as metals, topological insulators, and piezoelectrics.

Abstract—The miniaturization of semiconductor devices has reached the point where the number of a... more Abstract—The miniaturization of semiconductor devices has reached the point where the number of atoms is countable and geometries are formed in three dimensions. The Nanoelectronic Modeling tool suite NEMO5 is designed to comprehend the critical multi-scale, multi-physics phenomena and deliver results to engineers, scientists, and students through efficient computational approaches. Keywords: Atomistic Simulations; Nanoelectronic; Tightbinding; NEGF; Multiphysics; Multiscale; Parallel Computing.