Article
Biochemistry & Molecular Biology
David L. Cheung
Summary: Solid surfaces have a significant impact on the aggregation and assembly of biomolecular systems, with protein fibrillation being an important example. The molecular and oligomer structures adopted by proteins on surfaces play a crucial role in the rate of fibrillation. Molecular dynamics simulation is used in this study to investigate the aggregation of a model amyloidogenic peptide on a gold surface. The simulations reveal that the peptide adopts different conformations on the surface compared to bulk solution, resulting in significant differences in the formed oligomer structures. The adsorption of oligomers on the surface can also lead to restructuring, offering an explanation for the inhibition of fibrillation observed experimentally.
Article
Chemistry, Physical
Ipek Efe, Nicola A. Spaldin, Chiara Gattinoni
Summary: By using density functional theory, the study focuses on how the interaction between ferroelectric polarization and the chemical structure of bismuth ferrite (001) surfaces impacts the surface properties. The research reveals the most energetically favored surface geometries and the compensation mechanisms for charged surfaces, as well as suggests the potential of using the special surface properties of bismuth ferrite (001) for an effective water splitting cycle.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Cheng Zhu, Samuel E. Hoff, Miryana Hemadi, Hendrik Heinz
Summary: Understanding molecular interactions with metal surfaces is crucial for catalysts, sensors, and therapeutics. Obtaining accurate experimental data is a challenge and quantum-mechanical data is speculative. This study presents molecular dynamics simulations using the INTERFACE force field (IFF) to accurately predict adsorption energies and assembly of organic molecules on metal surfaces. The simulations show higher accuracy and faster speed than density functional calculations, reducing uncertainties and validating experimental data.
Article
Polymer Science
Leonid I. Klushin, Anna S. Ivanova, Alexey A. Polotsky, Alexander M. Skvortsov
Summary: We investigated the compression and interpenetration properties of two opposing monodisperse polymer brushes under external load using analytical theory and numerical self-consistent field (SCF) approach. We proposed analytical expressions for the brush density profiles and verified them using numerical SCF calculations. Interpenetration of the brushes was quantified using the penetration length, overlap integral Gamma, and the number of brush monomer units in the foreign half-space sigma. The interpenetration parameters were studied as functions of brush separation and external pressure. A theoretical description for the solvent-mediated friction force was also proposed in the low shearing rate regime. The total friction force, including direct brush-brush friction, was found to be expressed in terms of Gamma and sigma. Our SCF data showed that the interpenetration parameters and the total sliding friction force collapsed onto universal master curves when rescaled by (N/sigma)(1/3), where N is the chain length and sigma is the surface grafting density. The kinetic friction coefficient was defined as a function of external pressure, and its universal rescaled behavior was analyzed for the limits of non-draining and free-draining brushes.
Review
Chemistry, Applied
Yi Li, Fei Zhang
Summary: Self-assembly of metal halide perovskite nanocrystals holds significant application value in the fields of display, detector, and solar cell due to their unique collective properties. This review covers the driving forces, commonly used methods, and different self-assembly structures of perovskite nanocrystals. Additionally, it summarizes the collective optoelectronic properties and application areas of perovskite superlattice structures, and presents an outlook on potential issues and future challenges in the development of perovskite nanocrystals.
JOURNAL OF ENERGY CHEMISTRY
(2024)
Article
Engineering, Chemical
Ning Rui, Rui Shi, Ramon A. Gutierrez, Rina Rosales, Jindong Kang, Mausumi Mahapatra, Pedro J. Ramirez, Sanjaya D. Senanayake, Jose A. Rodriguez
Summary: The conversion and utilization of carbon dioxide is a critical challenge for reducing greenhouse gas pollution and producing high value chemicals. ZrO2/Cu(111) is an inverse oxide/metal catalyst with high activity and stability for the hydrogenation of CO2 into methanol, affecting the reaction products significantly.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2021)
Article
Multidisciplinary Sciences
Tamas Tarjanyi, Ferenc Bogar, Janos Minarovits, Mario Gajdacs, Zsolt Toth
Summary: The adhesion of biomolecules to dental and orthopedic implants is crucial for the process of osseointegration. Molecular dynamics simulations were performed to compare the adhesion properties of 6 peptides on different titanium dioxide surfaces. The residence time, pulling force, and binding energy of each peptide were calculated, and the adhesion strengths of the peptides were ranked based on the simulation results.
Article
Biochemical Research Methods
Robert E. Birdsall, Jacob Kellett, Samantha Ippoliti, Nilini Ranbaduge, Matthew A. Lauber, Ying Qing Yu, Weibin Chen
Summary: In this study, the performance of a column hardware with a novel hybrid silica surface in reducing metal-induced adsorption artifacts for acidic amino acid residue containing peptides was evaluated. The results demonstrated that the column effectively reduced peak tailing for peptides containing acidic residues.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Chemistry, Physical
Abolfazl Faeli Qadikolae, Sumit Sharma
Summary: Surfactant-metal interactions play a crucial role in corrosion inhibition and synthesis of metallic nanoparticles. In this study, we investigate the adsorption behavior of quaternary ammonium-based surfactant micelles at iron-water interfaces with partially or fully covered adsorbed surfactant molecules using atomistic simulations. We find that a micelle prefers to adsorb on a bare metal patch on a partially covered surface, while on a fully covered surface, it adsorbs on top of already adsorbed molecules and takes on a hemispherical shape. The adsorption free energy decreases with increasing coverage of surfactants on the iron-water interface.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Mindika Tilan Nayakasinghe, Jonathan Guerrero-Sanchez, Noboru Takeuchi, Francisco Zaera
Summary: The thermal chemistry of crotonaldehyde on polished polycrystalline copper disk was characterized using temperature-programmed desorption and reflection-absorption infrared spectroscopy, with results showing contrasting adsorption modes compared to a Pt(111) single crystal substrate. The adsorption was found to be weaker on copper compared to platinum, with different adsorption energies and configurations observed. The surface adsorption modes on these two metals could potentially impact selectivity in single-atom alloy hydrogenation catalysis.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Akinori Fukushima, Masaya Hirano, Ryuichi Sato
Summary: This study calculates the free energies of adsorption between a solid wall and various arginine derivatives in water using molecular dynamics simulations. The results show that the hydrophilicity of the solid wall and the hydrophobic group size of the amino acids significantly affect the adsorption free energy.
STRUCTURAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Krishan Kanhaiya, Hendrik Heinz
Summary: The interaction between gas molecules and metal/oxide surfaces is important in various applications. However, the dynamics of O2 at different timescales have not been well studied. In this research, we used molecular mechanics and molecular dynamics simulations to obtain accurate potential energy surfaces for the adsorption of O2 on different metal and oxide surfaces. This study provides insights into oxidation rates and parameters for oxide growth.
Article
Environmental Sciences
Yang Yao, Sen Zhang, Yuqing Shi, Mengqi Xu, Jiaquan Zhang, Yongming Zhang, Jun Zhao
Summary: Rapid urbanization has significantly increased the fragmentation and diversity of impervious surfaces in Shanghai, especially low and high impervious surfaces. Population density, unit area Gross Domestic Product (GDP), and the percentage of primary industry are the primary driving forces of landscape pattern change. The contribution of impervious surface configuration to water quality variations decreased from 68.7% to 46.4% in the period 2000-2010.
Article
Chemistry, Applied
Tong Lou, Xiuqin Bai, Xiaoyan He, Ying Yang, Chengqing Yuan
Summary: Biofouling is a serious issue in marine environments that can be addressed by modifying contact surfaces with antimicrobial peptides. This study utilized molecular dynamics simulations to analyze peptide attachment behaviors on different Al-based surfaces, finding that surface atom distribution and water molecules play key roles. Surface modification with active groups like amino, hydroxyl, and carboxyl was shown to effectively capture peptides, offering insights for developing new peptides for ship antifouling applications.
PROGRESS IN ORGANIC COATINGS
(2021)
Review
Chemistry, Multidisciplinary
Sarita Kolay, Dipankar Bain, Subarna Maity, Aarti Devi, Amitava Patra, Rodolphe Antoine
Summary: Studies on the self-assembly of metal nanoclusters (MNCs) are gaining importance due to their optical properties and potential applications. This article reviews recent achievements in the self-assembly chemistry of MNCs, including the underlying mechanism and crucial parameters, such as van der Waals forces, electrostatic interaction, and metallophilic interaction.
Article
Chemistry, Physical
K. G. Sprenger, Alaksh Choudhury, Joel L. Kaar, Jim Pfaendtner
JOURNAL OF PHYSICAL CHEMISTRY B
(2016)
Article
Chemistry, Multidisciplinary
K. G. Sprenger, Jim Pfaendtner
Article
Chemistry, Physical
Kovas Palunas, K. G. Sprenger, Tobias Weidner, Jim Pfaendtner
JOURNAL OF MOLECULAR LIQUIDS
(2017)
Article
Chemistry, Physical
Samantha R. Summers, K. G. Sprenger, Jim Pfaendtner, Jan Marchan, Michael F. Summers, Joel L. Kaar
JOURNAL OF PHYSICAL CHEMISTRY B
(2017)
Article
Chemistry, Multidisciplinary
K. G. Sprenger, Arushi Prakash, Gary Drobny, Jim Pfaendtner
Article
Chemistry, Physical
K. G. Sprenger, J. G. Plaks, J. L. Kaar, J. Pfaendtner
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2017)
Article
Biophysics
Josh Smith, Kayla G. Sprenger, Rick Liao, Andrea Joseph, Elizabeth Nance, Jim Pfaendtner
Article
Biochemistry & Molecular Biology
Arushi Prakash, K. G. Sprenger, Jim Pfaendtner
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2018)
Article
Chemistry, Multidisciplinary
Brittney Hellner, Sarah Alamdari, Harley Pyles, Shuai Zhang, Arushi Prakash, Kayla G. Sprenger, James J. De Yoreo, David Baker, Jim Pfaendtner, Francois Baneyx
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Multidisciplinary Sciences
Kayla G. Sprenger, Joy E. Louveau, Pranav M. Murugan, Arup K. Chakraborty
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemical Research Methods
Simone Conti, Victor Ovchinnikov, Jonathan G. Faris, Arup K. Chakraborty, Martin Karplus, Kayla G. Sprenger
Summary: This paper presents an agent-based model that allows for the in silico investigation of antibody evolution against a pathogen. The model provides insights into the evolution of broadly neutralizing antibodies against HIV and can guide the design of vaccines against highly mutable pathogens. The model uses actual antibody nucleotide sequences and treats antibody/pathogen interactions in atomistic detail.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Cardiac & Cardiovascular Systems
Dean Oldham, Hong Wang, Juliet Mullen, Emma Lietzke, Kayla Sprenger, Philip Reigan, Robert H. Eckel, Kimberley D. Bruce
Summary: This article introduces recently optimized methods for measuring LPL activity, providing cost-effective and reproducible methods for measuring LPL activity in human plasma and LPL-enriched cell fractions. It also describes methods using human serum as a source of endogenous activators and inhibitors, as well as high-throughput measurements of LPL activity using ApoC-II peptide and nAngptl4.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Immunology
Brian M. Petersen, Sophia A. Ulmer, Emily R. Rhodes, Matias F. Gutierrez-Gonzalez, Brandon J. Dekosky, Kayla G. Sprenger, Timothy A. Whitehead
Summary: Monoclonal antibodies are key therapeutics for cancer, inflammation, and infectious diseases. Natural human antibody repertoire-based scoring matrices can accurately predict mutations in therapeutic antibodies. High frequency mutations in natural human antibody repertoires have the potential to improve existing therapeutic antibodies and reduce immunogenicity.
FRONTIERS IN IMMUNOLOGY
(2021)
Proceedings Paper
Physics, Atomic, Molecular & Chemical
K. G. Sprenger, Yi He, Jim Pfaendtner
FOUNDATIONS OF MOLECULAR MODELING AND SIMULATION
(2016)