Digital Commons Network^™

Establishing Physical And Chemical Mechanisms Of Polymerization And Pyrolysis Of Phenolic Resins For Carbon-Carbon Composites, Ivan Gallegos, Josh Kemppainen, Jacob R. Gissinger, Malgorzata Kowalik, Adri Van Duin, Kristopher E. Wise, S. Gowtham, Gregory Odegard

Michigan Tech Publications, Part 2

The complex structural and chemical changes that occur during polymerization and pyrolysis critically affect material properties but are difficult to characterize in situ. This work presents a novel, experimentally validated methodology for modeling the complete polymerization and pyrolysis processes for phenolic resin using reactive molecular dynamics. The polymerization simulations produced polymerized structures with mass densities of 1.24 ± 0.01 g/cm3 and Young's moduli of 3.50 ± 0.64 GPa, which are in good agreement with experimental values. The structural properties of the subsequently pyrolyzed structures were also found to be in good agreement with experimental X-ray data for the phenolic-derived carbon …

From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …

Machine Learning Strategies For Potential Development In High-Entropy Driven Nickel-Based Superalloys, Marium Mostafiz Mou

MSU Graduate Theses

In this study, I developed Deep Learning interatomic potentials to model a multi-phase and multi-component system of Ni-based Superalloys. The system has up to three major phase constituents, namely Gamma, Gamma Prime, and Transition-metal rich Carbide. I utilized invariant scalar-based and/or equivariant, tensor-based neural network (NN) approach as implemented in DEEPMD, NEQUIP/ALLEGRO codes, respectively, and Moment Tensor Potential (MTP). For the training and validation sets, I employed the ab-initio molecular dynamics (AIMD) trajectory results and ground state DFT calculations, including the energy, force, and virial database from highly diverse compositions, temperatures, and pressures following a “High Entropy Strategy.” The Deep …

Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers

Legacy Theses & Dissertations (2009 - 2024)

Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …

Computer Simulations And Network-Based Profiling Of Binding And Allosteric Interactions Of Sars-Cov-2 Spike Variant Complexes And The Host Receptor: Dissecting The Mechanistic Effects Of The Delta And Omicron Mutations, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we combine all-atom MD simulations and comprehensive mutational scanning of S-RBD complexes with the angiotensin-converting enzyme 2 (ACE2) host receptor in the native form as well as the S-RBD Delta and Omicron variants to (a) examine the differences in the dynamic signatures of the S-RBD complexes and (b) identify the critical binding hotspots and sensitivity of the mutational positions. We also examined the differences in allosteric interactions and communications in the S-RBD complexes for the Delta and Omicron variants. Through the perturbation-based scanning of the allosteric propensities of the SARS-CoV-2 S-RBD residues and dynamics-based network centrality and …

Mdz: An Efficient Error-Bounded Lossy Compressor For Molecular Dynamics, Kai Zhao, Sheng Di, Danny Perez, Xin Liang, Zizhong Chen, Franck Cappello

Computer Science Faculty Research & Creative Works

Molecular dynamics (MD) has been widely used in today's scientific research across multiple domains including materials science, biochemistry, biophysics, and structural biology. MD simulations can produce extremely large amounts of data in that each simulation could involve a large number of atoms (up to trillions) for a large number of timesteps (up to hundreds of millions). In this paper, we perform an in-depth analysis of a number of MD simulation datasets and then develop an efficient error-bounded lossy compressor that can significantly improve the compression ratios. The contributions are fourfold. (1) We characterize a number of MD datasets and summarize …

Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan

University Honors Theses

Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …

Toward Improving Understanding Of The Structure And Biophysics Of Glycosaminoglycans, Elizabeth K. Whitmore

Electronic Theses and Dissertations

Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) that mediate PG bioactivities, including signal transduction, tissue morphogenesis, and matrix assembly. To understand GAG function, it is important to understand GAG structure and biophysics at atomic resolution. This is a challenge for existing experimental and computational methods because GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharides. Molecular dynamics (MD) simulations come close to overcoming this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies conformations from unbiased all-atom explicit-solvent MD simulations of short GAG polymers …

Equations Of State For Warm Dense Carbon From Quantum Espresso, Derek J. Schauss

Theses and Dissertations

Warm dense plasma is the matter that exists, roughly, in the range of 10,000 to 10,000,000 Kelvin and has solid-like densities, typically between 0.1 and 10 grams per centimeter. Warm dense fluids like hydrogen, helium, and carbon are believed to make up the interiors of many planets, white dwarfs, and other stars in our universe. The existence of warm dense matter (WDM) on Earth, however, is very rare, as it can only be created with high-energy sources like a nuclear explosion. In such an event, theoretical and computational models that accurately predict the response of certain materials are thus very …

Static And Dynamical Properties Of Multiferroics, Sayed Omid Sayedaghaee

Graduate Theses and Dissertations

Since the silicon industrial revolution in the 1950s, a lot of effort was dedicated to the research and development activities focused on material and solid-state sciences. As a result, several cutting-edge technologies are emerging including the applications of functional materials in the design and enhancement of novel devices such as sensors, highly capable data storage media, actuators, transducers, and several other types of electronic tools. In the last two decades, a class of functional materials known as multiferroics has captured significant attention because of providing a huge potential for new designs due to possessing multiple ferroic order parameters at the …

Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of …

Analysis The Nano Contact Force Of Single Crystal Copper In Contact And Separation Processes, Jianmeng Huang, Jingjing Chen

Journal of System Simulation

Abstract: On the basis of considering the adhesive force and copper substrate elastic-plastic deformation, the contact and separation processes between diamond indenter and copper substrate are simulated based on EAM and Morse potentials and Verlet algorithm. The results show that, when diamond indenter approaches slowly to copper substrate during the contact process, some atoms at the top level of substrate happened “snap back” phenomenon significantly due to the gravity became the main interaction force. Furthermore, it can be seen that the contact force and the accumulation phenomenon of dislocation atoms increase gradually with the increment of diamond displacements. During in …

Interaction Of Particle-Particle And Particle-Bubble In Water:Molecular Dynamics Simulation, Qingqun Luo, Jieming Yang

Journal of System Simulation

Abstract: Graphene and a bulk of gas were used to represent a part of particle and a part of bubble, respectively, and their interactions in liquid water with dissolved gas were simulated. Changes of the structural phase diagram, the gas density, and the potential of mean force were analyzed. The results show that the interactions of particle-particle and particle-bubble are both related to the nanobubble bridges therein. The forming processes of nanobubble bridges were shown in details. The range of nanobubble bridges and the energy change of the system were quantitatively calculated.

Polyacrylamide In Glycerol Solutions From An Atomistic Perspective Of The Energetics, Structure, And Dynamics, Scott D. Hopkins, Gideon K. Gogovi, Eric Weisel, Robert A. Handler, Estela Blaisten-Barojas

VMASC Publications

All-atom molecular dynamics is used to investigate the structural, energetic, and dynamical properties of polyacrylamide (PAM) oligomers of different lengths solvated in pure glycerol, a 90:10 glycerol–water mixture, and pure water. We predict that the oligomers’ globular structure is obtained only when the modeling strategy considers the solvent as a continuous background. Meanwhile, for all-atom modeled solvents, the glycerol solutions display a strong tendency of trapping the oligomers in instantaneous elongated random coiled structures that remain locked-in over tens of nanoseconds. In pure water, the oligomers acquire considerably shorter random coiled structures of increased flexibility. The all-atom force field, generalized …

Molecular Dynamics Simulations Of Dna-Functionalized Nanoparticle Building Blocks On Gpus, Tyler Landon Fochtman

Graduate Theses and Dissertations

This thesis discusses massively parallel molecular dynamics simulations of nBLOCKs using graphical processing units. nBLOCKs are nanoscale building blocks composed of gold nanoparticles functionalized with single-stranded DNA molecules. To explore greater simulation time scales we implement our nBLOCK computational model as an extension to the coarse grain molecular simulator oxDNA. oxDNA is parameterized to match the thermodynamics of DNA strand hybridization as well as the mechanics of single stranded DNA and double stranded DNA. In addition to an in-depth review of our implementation details we also provide results of the model validation and performance tests. These validation and performance tests …

Modeling Beta-Traces For Beta-Barrels From Cryo-Em Density Maps, Dong Si, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands …

A Statistical Analytical Model For Hydrophilic Electropore Characterization: A Comparison Study, P. Marracino, M. Liberti, P.T. Vernier, F. Apollonio

Bioelectrics Publications

Molecular dynamics (MD) simulations have proved to be a useful tool for unveiling many aspects of pore formation in lipid membranes under the influence of external electric fields. In order to compare the size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed for characterizing pore geometry and its evolution over time. In the present paper three different methodologies for evaluating electropore geometrical behavior will be compared: (i) the first allows analysis of the dimensions of the pore through an algorithm that uses a Monte Carlo simulated annealing …

The Anisotropy Of Hexagonal Close-Packed And Liquid Interface Free Energy Using Molecular Dynamics Simulations Based On Modified Embedded-Atom Method, Ebrahim Asadi, Mohsen Asle Zaeem

Materials Science and Engineering Faculty Research & Creative Works

This work aims to comprehensively study the anisotropy of the hexagonal close-packed (HCP)-liquid interface free energy using molecular dynamics (MD) simulations based on the modified-embedded atom method (MEAM). As a case study, all the simulations are performed for Magnesium (Mg). The solid-liquid coexisting approach is used to accurately calculate the melting point and melting properties. Then, the capillary fluctuation method (CFM) is used to determine the HCP-liquid interface free energy (γ) and anisotropy parameters. In CFM, a continuous order parameter is employed to accurately locate the HCP-liquid interface location, and the HCP symmetry-adapted spherical harmonics are used to expand γ …

Changing Cpu Frequency In Comd Proxy Application Offloaded To Intel Xeon Phi Co-Processors, Gary Lawson, Masha Sosonkina, Yuzhong Shen

Computational Modeling & Simulation Engineering Faculty Publications

Obtaining exascale performance is a challenge. Although the technology of today features hardware with very high levels of concurrency, exascale performance is primarily limited by energy consumption. This limitation has lead to the use of GPUs and specialized hardware such as many integrated core (MIC) co-processors and FPGAs for computation acceleration. The Intel Xeon Phi co-processor, built upon the MIC architecture, features many low frequency, energy efficient cores. Applications, even those which do not saturate the large vector processing unit in each core, may benefit from the energy-efficient hardware and software of the Xeon Phi. This work explores the energy …

Pattern Mining And Events Discovery In Molecular Dynamics Simulations Data, Shobhit Sandesh Shakya

LSU Doctoral Dissertations

Molecular dynamics simulation method is widely used to calculate and understand a wide range of properties of materials. A lot of research efforts have been focused on simulation techniques but relatively fewer works are done on methods for analyzing the simulation results. Large-scale simulations usually generate massive amounts of data, which make manual analysis infeasible, particularly when it is necessary to look into the details of the simulation results. In this dissertation, we propose a system that uses computational method to automatically perform analysis of simulation data, which represent atomic position-time series. The system identifies, in an automated fashion, the …

Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He

Computer Science Faculty Publications

Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM …

A Hybrid Framework Of Iterative Mapreduce And Mpi For Molecular Dynamics Applications, Shuju Bai

LSU Doctoral Dissertations

Developing platforms for large scale data processing has been a great interest to scientists. Hadoop is a widely used computational platform which is a fault-tolerant distributed system for data storage due to HDFS (Hadoop Distributed File System) and performs fault-tolerant distributed data processing in parallel due to MapReduce framework. It is quite often that actual computations require multiple MapReduce cycles, which needs chained MapReduce jobs. However, Design by Hadoop is poor in addressing problems with iterative structures. In many iterative problems, some invariant data is required by every MapReduce cycle. The same data is uploaded to Hadoop file system in …

Visualization Of Time-Varying Data From Atomistic Simulations And Computational Fluid Dynamics, Bidur Bohara

LSU Doctoral Dissertations

Time-varying data from simulations of dynamical systems are rich in spatio-temporal information. A key challenge is how to analyze such data for extracting useful information from the data and displaying spatially evolving features in the space-time domain of interest. We develop/implement multiple approaches toward visualization-based analysis of time-varying data obtained from two common types of dynamical simulations: molecular dynamics (MD) and computational fluid dynamics (CFD). We also make application case studies. Parallel first-principles molecular dynamics simulations produce massive amounts of time-varying three-dimensional scattered data representing atomic (molecular) configurations for material system being simulated. Rendering the atomic position-time series along with …

New Open Source Software For Building Molecular Dynamics Systems, Bruce Michael Allen

Electronic Theses and Dissertations

The context of this work is the development of open source software to support researchers to quickly build systems of molecules for molecular dynamics (MD) simulations. The goal is achieved through the integration of three open source programs by judicious modifications and creation of new source code, which allows the creation of molecular models, MD cells and the LAMMPS geometry input files. The software changes work together supporting an easy and intuitive process for simulation system creation. Creation of multiple MD cells for research simulations becomes quicker and provides needed standardization to the simulation process. The researcher can select from …

A Molecular Dynamics Simulation Based Principal Component Analysis Framework For Computation Of Multi-Scale Modeling Of Protein And Its Interaction With Solvent, Tao Wu

Dissertations

This dissertation presents a new computational framework for calculating the normal modes and interactions of proteins, macromolecular assemblies and surrounding solvents. The framework employs a combination of molecular dynamics simulation (MD) and principal component analysis (PCA). It enables the capture and visualization of the molecules' normal modes and interactions over time scales that are computationally challenging. It also provides a starting point for experimental and further computational studies of protein conformational changes.

A protein's function is sometimes linked to its conformational flexibility. Normal mode analysis (NMA) and various extensions of it have provided insights into the conformational fluctuations associated with …

Space-Time Multiresolution Approach To Atomistic Visualization, Dipesh Bhattarai

LSU Doctoral Dissertations

Time-varying three-dimensional positional atomistic data are rich in spatial and temporal information. The problem is to understand them. This work offers multiple approaches that enable such understanding. An interactive atomistic visualization system is developed integrating complex analyses with visualization to present the data on space-time multiresolution basis facilitating the information extraction and generate understanding. This work also shows the usefulness of such an integrated approach. The information obtained from the analyses represents the system at multiple length and time scales. Radial distribution function (RDF) provides a complete average spatial map of the distribution of the atoms in the system which …

Scalable Parallel Molecular Dynamics Algorithms For Organic Systems, Satyavani Vemparala

LSU Master's Theses

A scalable parallel algorithm, Macro-Molecular Dynamics (MMD), has been developed for large-scale molecular dynamics simulations of organic macromolecules, based on space-time multi-resolution techniques and dynamic management of distributed lists. The algorithm also includes the calculation of long range forces using Fast Multipole Method (FMM). FMM is based on the octree data structure, in which each parent cell is divided into 8 child cells and this division continues until the cell size is equal to the non-bonded interaction cutoff length. Due to constant number of operations performed at each stage of the octree, the FMM algorithm scales as O(N). Design and …