Physics Commons^™

Electromagnetic Theory And Applications, Nicholas Madamopoulos, George Kliros

Open Educational Resources

This book intends to provide both the fundamentals of Electromagnetics but also some practical applications of the concepts covered. Having taught electromagnetics for several years, the authors feel that many times the field of electromagnetics comes as “old” and often times students do not appreciate the concepts and their importance in everyday applications. The authors intend to accompany the EM concepts with life applications. Hence, students may see the direct impact of the knowledge they acquire through the study of the field of electromagnetics and better appreciate the field.

Perspectives On Determinism In Quantum Mechanics: Born, Bohm, And The “Quantal Newtonian” Laws, Viraht Sahni

Publications and Research

Quantum mechanics has a deterministic Schrödinger equation for the wave function. The Göttingen–Copenhagen statistical interpretation is based on the Born Rule that interprets the wave function as a “probability amplitude.” A precept of this interpretation is the lack of determinism in quantum mechanics. The Bohm interpretation is that the wave function is a source of a field experienced by the electrons, thereby attributing determinism to quantum theory. In this paper, we present a new perspective on such determinism. The ideas are based on the equations of motion or “Quantal Newtonian” Laws obeyed by each electron. These Laws, derived from …

Perspectives On Determinism In Quantum Mechanics: Born, Bohm, And The 'Quantal Newtonian' Laws, Viraht Sahni

Publications and Research

Quantum mechanics has a deterministic Schrödinger equation for the wave function. The Göttingen-Copenhagen statistical interpretation is based on the Born Rule that interprets the wave function as a ‘probability amplitude’. A precept of this interpretation is the lack of determinism in quantum mechanics. The Bohm interpretation is that the wave function is a source of a field experienced by the electrons, thereby attributing determinism to quantum theory. In this paper we present a new perspective on such determinism. The ideas are based on the equations of motion or ‘Quantal Newtonian’ Laws obeyed by each electron. These Laws, derived from the …

Improving The Electrostatic Design Of The Jefferson Lab 300 Kv Dc Photogun, S.A.K. Wijethunga, M. A. Mamun, R. Suleiman, C. Hernandez-Garcia, B. Bullard, J. R. Delayen, J. Grames, G. A. Krafft, G. Palacios-Serrano, M. Poelker

Physics Faculty Publications

The 300 kV DC high voltage photogun at Jefferson Lab was redesigned to deliver electron beams with a much higher bunch charge and improved beam properties. The original design provided only a modest longitudinal electric field (Ez) at the photocathode, which limited the achievable extracted bunch charge. To reach the bunch charge goal of approximately few nC with 75 ps full-width at half-maximum Gaussian laser pulse width, the existing DC high voltage photogun electrodes and anode–cathode gap were modified to increase Ez at the photocathode. In addition, the anode aperture was spatially shifted with respect to the beamline longitudinal axis …

Additive Modulation Of Dna-Dna Interactions By Interstitial Ions, Wei Meng, Raju Timsina, Abby Bull, Kurt Andresen, Xiangyun Qiu

Physics and Astronomy Faculty Publications

Quantitative understanding of biomolecular electrostatics, particularly involving multivalent ions and highly charged surfaces, remains lacking. Ion-modulated interactions between nucleic acids provide a model system in which electrostatics plays a dominant role. Using ordered DNA arrays neutralized by spherical cobalt3+ hexammine and Mg2+ ions, we investigate how the interstitial ions modulate DNA-DNA interactions. Using methods of ion counting, osmotic stress, and x-ray diffraction, we systematically determine thermodynamic quantities, including ion chemical potentials, ion partition, DNA osmotic pressure and force, and DNA-DNA spacing. Analyses of the multidimensional data provide quantitative insights into their interdependencies. The key finding of this study is that …

Syllabus Ee330 Electromagnetics, Nicholas Madamopoulos

Open Educational Resources

Concepts covered in the undergraduate electrical engineering class of electromagnetics

Merging Parallel-Plate And Levitation Actuators To Enable Linearity And Tunability In Electrostatic Mems, Mark Pallay, Ronald N. Miles, Shahrzad Towfighian

Mechanical Engineering Faculty Scholarship

In this study, a linear electrostatic MEMS actuator is introduced. The system consists of a MEMS cantilever beam with combined parallel-plate and electrostatic levitation forces. By using these two forcing methods simultaneously, the static response and natural frequency can be made to vary linearly with the voltage. The static response shows a linear increase of 90 nm/V and is maintained for more than 12μm of the tip displacement. The natural frequency shows a linear increase of 16 Hz/V and is maintained throughout a 2.9 kHz shift in the natural frequency. This wide range of linear displacement and frequency tunability is …

A Practical, Quantitative Electrostatics Experiment, Bryan K. Armentrout, Diego Castano

Chemistry and Physics Faculty Articles

An electrostatics experiment is presented that is practical, affordable, and quantitative. The equipment required is readily available and relatively inexpensive. The experiment relies on the electrostatic induction that results from a charged insulative plate in proximity to a conductive sphere. The experiment yields accessible results (a) under a variety of environmental conditions and results that (b) allow for quantitative analyses. These two characteristics distinguish it from most other simple electrostatics experiments. It is intended for college introductory physics students.

Studying The Interface Between Croconic Acid Thin Films And Substrates Using A Slow Positron Beam, Dean Peterson, Jiandang Liu, Jonas Etzweiler, Gabriel Sontoyo, Sara J. Callori, Kimberley R. Cousins, Timothy Usher, Renwu Zhang

Physics Faculty Publications

Croconic acid (CA) is the first organic ferroelectric with a spontaneous polarity in bulk samples comparable to its inorganic counterparts. As a natural extension of study, ultrathin CA films (∼nm scale) were investigated to reveal ferroelectric effects in films on different substrates for their fundamental and industrial significance. However, the void defect at the interface between the film and substrate is presumed to interfere with surface effects. In this work, a non-invasive technique, a slow positron beam, coupled with Doppler broadening energy spectroscopy (DBES), is applied to study the void defects within the interfacial layer between CA films and Si …

Electrostatic Alignment Of Electrospun Peo Fibers By The Gap Method Increases Individual Fiber Modulus In Comparison To Non-Aligned Fibers Of Similar Diameter, Christopher Fryer, Meghan Scharnagl, Christine C. Helms

Physics Faculty Publications

Studies on the alignment, physical and mechanical properties of individual electrospun fibers provide insight to their formation, production and optimization. Here we measure the alignment, diameter and modulus of individual fibers formed using the electrostatic gap method. We find electrostatic alignment produces fibers with a smaller diameter than their nonaligned counterparts have. Therefore, due to the dependence of fiber modulus on diameter aligned fibers have a higher modulus. Furthermore, we show that aligned and nonaligned fibers of the similar diameter have different moduli. Aligned fibers have a modulus 1.5 to 2 times larger than nonaligned fibers of the similar diameter.

The Mechanism Of Plasma Plume Termination For Pulse Excited Plasmas In A Quartz Tube, Mingzhe Rong, Wenjie Xia, Xiaohua Wang, Zhijie Liu, Dingxin Liu, Zhihu Liang, Xiaoning Zhang, Michael G. Kong

Bioelectrics Publications

Although the formation and propagation of plasma plume for atmospheric pressure plasmas have been intensively studied, how does the plasma plume terminate is still little known. In this letter, helium plasma plumes are generated in a long quartz tube by pulsed voltages and a constant gas flow. The voltages have a variable pulse width (PW) from 0.5 μs to 200 μs. It is found that the plasma plume terminates right after the falling edge of each voltage pulse when PW < 20 μs, whereas it terminates before the falling edge. When PW is larger than 30 μs, the …

The Impact Of Base Stacking On The Conformations And Electrostatics Of Single-Stranded Dna, Alex Plumridge, Steve P. Meisburger, Kurt Andresen, Lois Pollack

Physics and Astronomy Faculty Publications

Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy …

Electrostatics At The Molecular Level, Ulrich Zurcher

Physics Faculty Publications

In molecular systems, positive and negative charges are separated, making them ideal systems to examine electrostatic interactions. The attractive force between positive and negative charges is balanced by repulsive ‘forces’ that are quantum-mechanical in origin. We introduce an ‘effective’ potential energy that captures the repulsion; it allows us to obtain fairly accurate estimates of the bonding properties of molecular systems. We use units (e.g., kcal mol–1 for energy) that emphasize the relevance of electrostatics to macroscopic behavior.

Beyond The Point Charge: Equipotential Surfaces And Electric Fields Of Various Charge Configurations, Jeffrey A. Phillips, Jeff Sanny, David Berube, Anatol Hoemke

Physics Faculty Works

A laboratory experiment often performed in an introductory electricity and magnetism course involves the mapping of equipotential lines on a conductive sheet between two objects at different potentials. In this article, we describe how we have expanded this experiment so that it can be used to illustrate the electrostatic properties of conductors. Different configurations of electrodes can be used to show that the electric field is zero inside a conductor as well as within a cavity, the electric field is perpendicular to conducting surfaces, and the charge distribution on conducting surfaces can vary.

Dirac Hamiltonian And Reissner-Nordström Metric: Coulomb Interaction In Curved Space-Time, J. H. Noble, Ulrich D. Jentschura

Physics Faculty Research & Creative Works

We investigate the spin-1/2 relativistic quantum dynamics in the curved space-time generated by a central massive charged object (black hole). This necessitates a study of the coupling of a Dirac particle to the Reissner-Nordström space-time geometry and the simultaneous covariant coupling to the central electrostatic field. The relativistic Dirac Hamiltonian for the Reissner-Nordström geometry is derived. A Foldy-Wouthuysen transformation reveals the presence of gravitational and electrogravitational spin-orbit coupling terms which generalize the Fokker precession terms found for the Dirac-Schwarzschild Hamiltonian, and other electrogravitational correction terms to the potential proportional to αⁿG, where α is the fine-structure constant and …

On The Modeling Of Polar Component Of Solvation Energy Using Smooth Gaussian-Based Dielectric Function, Lin Li, Chuan Li, Emil Alexov

Publications

Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine …

On The Electrostatic Properties Of Homodimeric Proteins, Brandon Campbell, Marharyta Petukh, Emil Alexov, Chuan Li

Publications

A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily …

Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov

Publications

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization …

The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov

Publications

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound …

In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov

Publications

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that …

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …

Highly Efficient And Exact Method For Parallelization Of Grid-Based Algorithms And Its Implementation In Delphi, Chuan Li, Lin Li, Jie Zhang, Emil Alexov

Publications

The Gauss–Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In …

Effects Of Long-Range Tip-Sample Interaction On Magnetic Force Imaging: A Comparative Study Between Bimorph Driven System And Electrostatic Force Modulation, Byung I. Kim

Physics Faculty Publications and Presentations

Magnetic force microscopy (MFM) using electrostatic force modulation has been designed and developed to avoid the drawbacks of the bimorph driven system. The bimorph driven system has poor frequency response and overlap of the topographic features on magnetic structures of the MFM images. In the electrostatic force modulation system, the amplitude increases in the noncontact regime as the tip approaches due to the capacitive coupling between tip and sample. MFM using electrostatic force modulation has been applied to observe maze-like stripe domain structures on a CoCr film. The contrast mechanism and imaging stability of MFM using electrostatic force modulation are …

Delphi: A Comprehensive Suite For Delphi Software And Associated Resources, Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov

Publications

Background

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.

Results

Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding …

Conformational Temperature-Dependent Behavior Of A Histone H2ax: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials, Miriam Fritsche, Ras B. Pandey, Barry L. Farmer, Dieter W. Heerman

Faculty Publications

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input …

Developing Hybrid Approaches To Predict Pka Values Of Ionizable Groups, Shawn Witham, Kemper Talley, Lin Wang, Zhe Zhang, Daquan Gao, Wei Yang, Emil Alexov

Publications

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid …

A Missense Mutation In Clic2 Associated With Intellectual Disability Is Predicted By In Silico Modeling To Affect Protein Stability And Dynamics, Shawn Witham, Kyoko Takano, Charles Schwartz, Emil Alexov

Publications

Large-scale next generation resequencing of X chromosome genes identified a missense mutation in the CLIC2 gene on Xq28 in a male with X-linked intellectual disability (XLID) and not found in healthy individuals. At the same time, numerous nsSNPs (nonsynonomous SNP) have been reported in the CLIC2 gene in healthy individuals indicating that the CLIC2 protein can tolerate amino acid substitutions and be fully functional. To test the possibility that p.H101Q is a disease-causing mutation, we performed in silico simulations to calculate the effects of the p.H101Q mutation on CLIC2 stability, dynamics, and ionization states while comparing the effects obtained for …

In Silico Modeling Of Ph-Optimum Of Protein-Protein Binding, Rooplekha C. Mitra, Zhe Zhang, Emil Alexov

Publications

Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity …

Tunneling Electroresistance In Ferroelectric Tunnel Junctions With A Composite Barrier, M. Ye. Zhuravlev, Yong Wang, S. Maekawa, Evgeny Y. Tsymbal

Evgeny Tsymbal Publications

Tunneling electroresistance (TER) effect is the change in the electrical resistance of a ferroelectric tunnel junction (FTJ) associated with polarization reversal in the ferroelectric barrier layer. Here we predict that a FTJ with a composite barrier that combines a functional ferroelectric film and a thin layer of a nonpolar dielectric can exhibit a significantly enhanced TER. Due to the change in the electrostatic potential with polarization reversal, the nonpolar dielectric barrier acts as a switch that changes its barrier height from a low to high value. The predicted values of TER are giant and indicate that the resistance of the …

Separation Of Topographic Features From Magnetic Force Images Using Capacitive Coupling Effect, Byung I. Kim

Physics Faculty Publications and Presentations

Separation of topographic features from magnetic images has been an issue for the past two decades in magnetic force microscopy (MFM). The frequent pickups of the topographic features are interpreted as transitions of the tip between bistable states of the tip-sample assembly in the noncontact and tapping regions. MFM using electrostatic force modulation demonstrates the separation of the topographic features from the magnetic images by removing the tapping state from the bistable states through the introduction of a capacitive coupling.