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Full-Text Articles in Physics

Computational Studies Of Thermal Properties And Desalination Performance Of Low-Dimensional Materials, Yang Hong Aug 2019

Computational Studies Of Thermal Properties And Desalination Performance Of Low-Dimensional Materials, Yang Hong

Student Research Projects, Dissertations, and Theses - Chemistry Department

During the last 30 years, microelectronic devices have been continuously designed and developed with smaller size and yet more functionalities. Today, hundreds of millions of transistors and complementary metal-oxide-semiconductor cells can be designed and integrated on a single microchip through 3D packaging and chip stacking technology. A large amount of heat will be generated in a limited space during the operation of microchips. Moreover, there is a high possibility of hot spots due to non-uniform integrated circuit design patterns as some core parts of a microchip work harder than other memory parts. This issue becomes acute as stacked microchips get ...


Predicting The Mechanical Properties Of Nanocomposites Reinforced With 1-D, 2-D And 3-D Nanomaterials, Scott Edward Muller May 2019

Predicting The Mechanical Properties Of Nanocomposites Reinforced With 1-D, 2-D And 3-D Nanomaterials, Scott Edward Muller

Theses and Dissertations

Materials with features at the nanoscale can provide unique mechanical properties and increased functionality when included as part of a nanocomposite. This dissertation utilizes computational methods at multiple scales, including molecular dynamics (MD) and density functional theory (DFT), and the coupled atomistic and discrete dislocation multiscale method (CADD), to predict the mechanical properties of nanocomposites possessing nanomaterials that are either 1-D (carbyne chains), 2-D (graphene sheets), or 3-D (Al/amorphous-Si core-shell nanorod).

The MD method is used to model Ni-graphene nanocomposites. The strength of a Ni-graphene nanocomposite is found to improve by increasing the gap between the graphene sheet and ...


Polymer Infiltration Under Extreme Confinement, David Ring Jan 2019

Polymer Infiltration Under Extreme Confinement, David Ring

Publicly Accessible Penn Dissertations

Polymer nanocomposites with high nanoparticle loadings are ubiquitous in nature but difficult to replicate synthetically. A simple technique to create such polymer nanocomposites is to form a bi-layer of a nanoparticle thin film atop a polymer thin film and anneal above the polymer glass transition temperature to induce wicking. This Capillary Rise Infiltration (CaRI) of polymers into nanoparticle thin films is a promising method to create interesting biomimetic composites with enhanced material properties, but also raises important theoretical questions about confinement, capillarity, and polymer dynamics. Therefore, I use molecular dynamics simulations (MD) and continuum theory to understand the impact of ...


Real-Time Observation Of Molecular Spinning With Angular High-Harmonic Spectroscopy, Lixin He, Pengfei Lan, Anh-Thu Le, Baoning Wang, Bincheng Wang, Xiaosong Zhu, Peixiang Lu, C. D. Lin Oct 2018

Real-Time Observation Of Molecular Spinning With Angular High-Harmonic Spectroscopy, Lixin He, Pengfei Lan, Anh-Thu Le, Baoning Wang, Bincheng Wang, Xiaosong Zhu, Peixiang Lu, C. D. Lin

Physics Faculty Research & Creative Works

We demonstrate an angular high-harmonic spectroscopy method to probe the spinning dynamics of a molecular rotation wave packet in real time. With the excitation of two time-delayed, polarization-skewed pump pulses, the molecular ensemble is impulsively kicked to rotate unidirectionally, which is subsequently irradiated by another delayed probe pulse for high-order harmonic generation (HHG). The spatiotemporal evolution of the molecular rotation wave packet is visualized from the time-dependent angular distributions of the HHG yields and frequency shift measured at various polarization directions and time delays of the probe pulse. The observed frequency shift in HHG is demonstrated to arise from the ...


Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman Aug 2018

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation ...


Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru May 2018

Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru

University Scholar Projects

Though eradicated in most of the world, poliovirus remains a common model virus for a family of mammalian viruses known as Picornaviruses. Despite the development of a vaccination, little is understood about the infection process, particularly the mechanism of cell entry. Experimental studies have attempted to elucidate the dynamics of this process and have proposed pathways focused on VP4, the smallest of the four peptides which makes up the viral capsid, and its interaction with the pentameric interfaces of the five fold axes. This study utilizes coarse-grained molecular dynamics to supplement these proposed mechanisms with simplified simulations which reduce the ...


Implementation Of Metal-Friendly Eam/Fs-Type Semi-Empirical Potentials In Hoomd-Blue: A Gpu-Accelerated Molecular Dynamics Software, Lin Yang, Feng Zhang, Cai-Zhuang Wang, Kai-Ming Ho, Alex Travesset Apr 2018

Implementation Of Metal-Friendly Eam/Fs-Type Semi-Empirical Potentials In Hoomd-Blue: A Gpu-Accelerated Molecular Dynamics Software, Lin Yang, Feng Zhang, Cai-Zhuang Wang, Kai-Ming Ho, Alex Travesset

Ames Laboratory Accepted Manuscripts

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu64.5Zr35.5, and pair correlation function of liquid Ni3Al. Our code scales well with the size of the simulating system on ...


Phase Transitions And Their Interaction With Dislocations In Silicon, Valery I. Levitas, Hao Chen, Liming Xiong Jan 2018

Phase Transitions And Their Interaction With Dislocations In Silicon, Valery I. Levitas, Hao Chen, Liming Xiong

Aerospace Engineering Publications

In this paper, phase transformations (PTs) in silicon were investigated through molecular dynamics (MD) using Tersoff potential. In the first step, simulations of PTs in single crystal silicon under various stress-controlled loading were carried out. Results shows that all instability points under various stress states are described by criteria, which are linear in the space of normal stresses. There is a region in the stress space in which conditions for direct and reverse PTs coincide and a unique homogeneous phase transition (without nucleation) can be realized. Finally, phase transition in bi-crystalline silicon with a dislocation pileup along the grain boundary ...


Cooling Rate Dependence Of Structural Order In Ni62nb38 Metallic Glass, Tongqi Wen, Yang Sun, Beilin Ye, Ling Tang, Zejin Yang, Kai-Ming Ho, Cai-Zhuang Wang, Nan Wang Jan 2018

Cooling Rate Dependence Of Structural Order In Ni62nb38 Metallic Glass, Tongqi Wen, Yang Sun, Beilin Ye, Ling Tang, Zejin Yang, Kai-Ming Ho, Cai-Zhuang Wang, Nan Wang

Ames Laboratory Accepted Manuscripts

Molecular dynamics (MD) simulations are performed to study the structure of Ni62Nb38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni62Nb38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfect icosahedra is driven by chemical ordering in ...


Structures And Dynamics Investigation Of Phase Selection In Metallic Alloy Systems, Lin Yang Jan 2018

Structures And Dynamics Investigation Of Phase Selection In Metallic Alloy Systems, Lin Yang

Graduate Theses and Dissertations

Different phases of metallic alloys have a wide range of applications. However, the driving mechanisms of the phase selections can be complex. For example, the detailed pathways of the phase transitions in the devitrification process still lack a comprehensive interpretation. So, the understanding of the driving mechanisms of the phase selections is very important.

In this thesis, we focus on the study of the Al-Sm and other related metallic alloy systems by simulation and experiment. A procedure to evaluate the free energy has been developed within the framework of thermodynamic integration, coupled with extensive GPU-accelerated molecular dynamics (MD) simulations; The ...


Transport Of Water And Ions Through Single-Walled Armchair Carbon Nanotubes: A Molecular Dynamics Study, Michelle Patricia Aranha Dec 2017

Transport Of Water And Ions Through Single-Walled Armchair Carbon Nanotubes: A Molecular Dynamics Study, Michelle Patricia Aranha

Doctoral Dissertations

The narrow hydrophobic interior of a carbon nanotube (CNT) poses a barrier to the transport of water and ions, and yet, unexpectedly, numerous experimental and simulation studies have confirmed fast water transport rates comparable to those seen in biological aquaporin channels. These outstanding features of high water permeability and high solute rejection of even dissolved ions that would typically require a lot of energy for separation in commercial processes makes carbon nanotubes an exciting candidate for desalination membranes. Extending ion exclusion beyond simple mechanical sieving by the inclusion of electrostatics via added functionality to the nanotube bears promise to not ...


Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw Nov 2017

Entropy Production And Volume Contraction In Thermostated Hamiltonian Dynamics, John D. Ramshaw

Physics Faculty Publications and Presentations

Patra et al. [Int. J. Bifurcat. Chaos 26, 1650089 (2016)] recently showed that the time-averaged rates of entropy production and phase-space volume contraction are equal for several different molecular dynamics methods used to simulate nonequilibrium steady states in Hamiltonian systems with thermostated temperature gradients. This equality is a plausible statistical analog of the second law of thermodynamics. Here we show that those two rates are identically equal in a wide class of methods in which the thermostat variables z are determined by ordinary differential equations of motion (i.e., methods of the Nosé-Hoover or integral feedback control type). This class ...


Characterization Of Hydrophobic Interactions Of Polymers With Water And Phospholipid Membranes Using Molecular Dynamics Simulations, Mihaela Drenscko Sep 2017

Characterization Of Hydrophobic Interactions Of Polymers With Water And Phospholipid Membranes Using Molecular Dynamics Simulations, Mihaela Drenscko

All Dissertations, Theses, and Capstone Projects

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid ...


Overview Of Weighted Ensemble Simulation: Path-Sampling, Steady States, Equilibrium, Daniel M. Zuckerman May 2017

Overview Of Weighted Ensemble Simulation: Path-Sampling, Steady States, Equilibrium, Daniel M. Zuckerman

Scholar Archive

A concise overview of the weighted ensemble path sampling method for rare events is given, aimed at beginners.


Molecular Simulations Of Protein-Induced Membrane Remodeling, Ryan Patrick Bradley Jan 2016

Molecular Simulations Of Protein-Induced Membrane Remodeling, Ryan Patrick Bradley

Publicly Accessible Penn Dissertations

Membranes organize much of the cell and host a great deal of molecular machinery required to integrate signals from the outside, regulate the surrounding matrix, change shape, move, and grow. Understanding how a dense forest of proteins, sugars, and biomarkers modulates the shape of the cell is necessary to produce more detailed, accurate predictions of cell behavior, particularly in the studies of cell signaling processes that lead to oncogenesis. In this dissertation, I will present a series of molecular models which, when combined with continuum models and both in vitro and in vivo experiments, describe the molecular basis for membrane ...


Molecular Mechanisms Of Protein Thermal Stability, Lucas Sawle Jan 2016

Molecular Mechanisms Of Protein Thermal Stability, Lucas Sawle

Electronic Theses and Dissertations

Organisms that thrive under extreme conditions, such as high salt concentration, low pH, or high temperature, provide an opportunity to investigate the molecular and cellular strategies these organisms have adapted to survive in their harsh environments. Thermophilic proteins, those extracted from organisms that live at high temperature, maintain their structure and function at much higher temperatures compared to their mesophilic counterparts, found in organisms that live near room temperature. Thermophilic and mesophilic homolog protein pairs have identical functionality, and show a high degree of structural and sequential similarity, but differ significantly in their response to high temperature. Addressing the principles ...


Using Dissipative Particle Dynamics For Modeling Surfactants, Yuchen Zhang, Arezoo M. Ardekani Aug 2015

Using Dissipative Particle Dynamics For Modeling Surfactants, Yuchen Zhang, Arezoo M. Ardekani

The Summer Undergraduate Research Fellowship (SURF) Symposium

Oil recovery is an industrial process that injects aqueous solutions into an oil reservoir to pump out crude oil and promote the oil production. The aqueous solution contains surfactants for reducing the interfacial tension (IFT) between aqueous phase and oil. The critical micelle concentration (CMC) is the concentration of surfactant above which micelles form and the interfacial tension reaches a plateau. Our research seeks to measure IFT and CMC for surfactants using dissipative particle dynamics (DPD) technique, which is a coarse-grained method based on the molecular dynamics. We first study how IFT is influenced by the surfactant concentration. Furthermore, another ...


Statistical Biophysics Blog: “Proof” Of The Hill Relation Between Probability Flux And Mean First-Passage Time, Daniel M. Zuckerman Apr 2015

Statistical Biophysics Blog: “Proof” Of The Hill Relation Between Probability Flux And Mean First-Passage Time, Daniel M. Zuckerman

Scholar Archive

The “Hill relation” is a key result for anyone interested in calculating rates from trajectories of any kind, whether molecular simulations or otherwise. I am not aware of any really clear explanation, including Hill’s original presentation. Hopefully this go-around will make sense.


Effects Of Schmid Factor And Slip Nucleation On Deformation Mechanism In Columnar-Grained Nanotwinned Ag And Cu, Valery Borovikov, Mikhail I. Mendelev, Alexander H. King, Richard Lesar Jan 2015

Effects Of Schmid Factor And Slip Nucleation On Deformation Mechanism In Columnar-Grained Nanotwinned Ag And Cu, Valery Borovikov, Mikhail I. Mendelev, Alexander H. King, Richard Lesar

Ames Laboratory Publications

We report the results of a molecular dynamics study of the effect of texture on the yield and peak stresses in columnar-grained nanotwinned Ag and Cu. The simulations suggest that in pure nanotwinned face-centered cubic metals, the strength is determined primarily by the cooperation or competition between two major factors: the magnitude of the Schmid factors for the available slip systems and the effectiveness of grain boundaries (and their triple-junctions) in generating dislocations. These factors and their relative impact depend on the geometry of the specimen relative to the applied stress, which is typically reflected in the texture of the ...


The Interaction Mechanisms Of A Screw Dislocation With A Defective Coherent Twin Boundary In Copper, Qiongjiali Fang Jan 2015

The Interaction Mechanisms Of A Screw Dislocation With A Defective Coherent Twin Boundary In Copper, Qiongjiali Fang

Graduate College Dissertations and Theses

Σ3{111} coherent twin boundary (CTB) in face-centered-cubic (FCC) metals and alloys have been regarded as an efficient way to simultaneously increase strength and ductility at the nanoscale. Extensive study of dislocation-CTB interaction has been carried out by a combination of computer simulations, experiments and continuum theory. Most of them, however, are based on the perfect CTB assumption. A recent study [Wang YM, Sansoz F, LaGrange T, et al. Defective twin boundaries in nanotwinned metals. Nat Mater. 2013;12(8):697-702.] has revealed the existence of intrinsic kink-like defects in CTBs of nanotwinned copper through nanodiffraction mapping technique, and has ...


Scaling And Alpha-Helix Regulation Of Protein Relaxation In A Lipid Bilayer, Liming Qiu, Creighton Buie, Kwan H. Cheng, Mark W. Vaughn Dec 2014

Scaling And Alpha-Helix Regulation Of Protein Relaxation In A Lipid Bilayer, Liming Qiu, Creighton Buie, Kwan H. Cheng, Mark W. Vaughn

Physics and Astronomy Faculty Research

Protein conformation and orientation in the lipid membrane plays a key role in many cellular processes. Here we use molecular dynamics simulation to investigate the relaxation and C-terminus diffusion of a model helical peptide: beta-amyloid (Aβ) in a lipid membrane.We observed that after the helical peptide was initially half-embedded in the extracelluar leaflet of phosphatidylcholine (PC) or PC/cholesterol (PC/CHOL) membrane, the C-terminus diffused across the membrane and anchored to PC headgroups of the cytofacial lipid leaflet. In some cases, the membrane insertion domain of the Aβ was observed to partially unfold. Applying a sigmoidal fit to the ...


Statistical Mechanical Models For Dissociative Adsorption Of O2 On Metal(100) Surfaces With Blocking, Steering, And Funneling, Da-Jiang Liu, James W. Evans May 2014

Statistical Mechanical Models For Dissociative Adsorption Of O2 On Metal(100) Surfaces With Blocking, Steering, And Funneling, Da-Jiang Liu, James W. Evans

Physics and Astronomy Publications

We develop statistical mechanical models amenable to analytic treatment for the dissociative adsorption of O2 at hollow sites on fcc(100) metal surfaces. The models incorporate exclusion of nearest-neighbor pairs of adsorbed O. However, corresponding simple site-blocking models, where adsorption requires a large ensemble of available sites, exhibit an anomalously fast initial decrease in sticking. Thus, in addition to blocking, our models also incorporate more facile adsorption via orientational steering and funneling dynamics (features supported by ab initio Molecular Dynamics studies). Behavior for equilibrated adlayers is distinct from those with finite adspecies mobility. We focus on the low-temperature limited-mobility regime ...


Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi Mar 2014

Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi

FIU Electronic Theses and Dissertations

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions ...


Lattice Thermal Conductivity In Bulk And Nanosheet Naxcoo2, Denis Demchenko, David B. Ameen Jan 2014

Lattice Thermal Conductivity In Bulk And Nanosheet Naxcoo2, Denis Demchenko, David B. Ameen

Physics Publications

In this paper we present the results of calculations of the lattice thermal conductivity of layered complex metal oxide NaxCoO2 within the Green–Kubo theory. Using NaxCoO2 we identify the two competing mechanisms responsible for the favorable scaling properties of the Green–Kubo method for calculating the lattice thermal conductivity. The artificial correlations of the heat flux fluctuations due to the finite size of the supercells are partially cancelled by the missing long wavelength acoustic phonon modes. We compute the lattice thermoelectric properties of bulk NaxCoO2 with varying stoichiometry, structural defects ...


Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell Jan 2014

Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell

Faculty Publications

We formulate low Mach number fluctuating hydrodynamic equations appropriate for modeling diffusive mixing in isothermal mixtures of fluids with different density and transport coefficients. These equations eliminate the fast isentropic fluctuations in pressure associated with the propagation of sound waves by replacing the equation of state with a local thermodynamic constraint. We demonstrate that the low Mach number model preserves the spatio-temporal spectrum of the slower diffusive fluctuations. We develop a strictly conservative finite-volume spatial discretization of the low Mach number fluctuating equations in both two and three dimensions. We construct several explicit Runge-Kutta temporal integrators that strictly maintain the ...


Tunable Surface Hydrophobicity And Fluid Transport Through Nanoporous Membranes, Joseph H.J. Ostrowski Jan 2014

Tunable Surface Hydrophobicity And Fluid Transport Through Nanoporous Membranes, Joseph H.J. Ostrowski

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

There are more than three billion people across the globe that struggle to obtain clean drinkable water. One of the most promising avenues for generating potable water is through reverse osmosis and nanofiltration. Both solutions require a semipermeable membrane that prohibits passage of unwanted solute particles but allows passage of the solvent. Atomically thin two-dimensional membranes based on porous graphene show great promise as semipermeable materials, but modeling fluid flow on length scales between the microscopic (nanometer and smaller) and macroscopic (micron and larger) regimes presents formidable challenges. This thesis explores both equilibrium and nonequilibrium aspects of this problem and ...


High Harmonic Driven Attosecond And Femtosecond Molecular Dynamics, William Craig Hogle Jan 2014

High Harmonic Driven Attosecond And Femtosecond Molecular Dynamics, William Craig Hogle

Physics Graduate Theses & Dissertations

To fully understand atomic and molecular dynamics scientists must be able to probe and study dynamics on their fundamental time scales. The motion, structure, and arrangement of molecules play a fundamental role in chemical reactions. Analyzing these reactions is not only important for their immediate insights but the understanding is essential for the progress of many areas of science and technology including biology, material science, and medicine.

These dynamics require a light source with not only the time resolution to capture attosecond and femtosecond dynamics but one that can also reach a large energy range of interesting processes. High harmonic ...


Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell Dec 2013

Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell

Alejandro Garcia

We formulate low Mach number fluctuating hydrodynamic equations appropriate for modeling diffusive mixing in isothermal mixtures of fluids with different density and transport coefficients. These equations eliminate the fast isentropic fluctuations in pressure associated with the propagation of sound waves by replacing the equation of state with a local thermodynamic constraint. We demonstrate that the low Mach number model preserves the spatio-temporal spectrum of the slower diffusive fluctuations. We develop a strictly conservative finite-volume spatial discretization of the low Mach number fluctuating equations in both two and three dimensions. We construct several explicit Runge-Kutta temporal integrators that strictly maintain the ...


Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega May 2013

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose ...


Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier Apr 2013

Electric Field-Driven Water Dipoles: Nanoscale Architecture Of Electroporation, Mayya Tokman, Jane Hyojin Lee, Zachary A. Levine, Ming-Chak Ho, Michael E. Colvin, P. Thomas Vernier

Bioelectrics Publications

Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensively in biology, biotechnology, and medicine, its molecular mechanism is not well understood. This lack of knowledge limits the ability to control and fine-tune the process. In this article we propose a novel molecular mechanism for the electroporation of a lipid bilayer based on energetics analysis. Using molecular dynamics simulations we demonstrate that ...