Article
Chemistry, Medicinal
Lane W. Votapka, Andrew M. Stokely, Anupam A. Ojha, Rommie E. Amaro
Summary: SEEKR2 is a computational method for estimating the kinetics and thermodynamics of molecular processes. It provides equivalent or improved results compared to previous versions, with increased speed and capabilities. SEEKR2 also offers improved usability and supports simulation using OpenMM and Browndye 2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Nicholas M. Gravina, James C. Gumbart, Harold D. Kim
Summary: This study investigates the interactions between DNA sticky ends using the coarse-grained oxDNA model, finding that the orientation of double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind. Specifically, the binding time is fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Andrey Sarikov, Anna Marzegalli, Luca Barbisan, Massimo Zimbone, Corrado Bongiorno, Marco Mauceri, Danilo Crippa, Francesco La Via, Leo Miglio
Summary: The annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates was studied using molecular dynamics simulations. Two SF annihilation scenarios were revealed under slightly compressive strain conditions, showing how the interaction of partial dislocations affects the evolution of SFs. These results provide insights into the reduction of SF concentrations in epitaxial 3C-SC layers on Si substrates.
Article
Chemistry, Multidisciplinary
Susanna M. Frueh, Ulf Matti, Philipp R. Spycher, Marina Rubini, Sebastian Lickert, Thomas Schlichthaerle, Ralf Jungmann, Viola Vogel, Jonas Ries, Ingmar Schoen
Summary: In this study, a simple two-step protocol was developed to site-specifically attach reporters to IgG antibodies, and their performance in super-resolution microscopy techniques was evaluated. The results showed that errors from primary and secondary antibodies did not add up, and simulations revealed the main factors contributing to the errors.
Article
Chemistry, Physical
Anthony J. J. Cooper, Michael P. P. Howard, Sanket Kadulkar, David Zhao, Kris T. T. Delaney, Venkat Ganesan, Thomas M. M. Truskett, Glenn H. H. Fredrickson
Summary: We have developed a multiscale simulation model for predicting solute diffusion through porous triblock copolymer membranes. The model combines self-consistent field theory (SCFT) and on-lattice kinetic Monte Carlo (kMC) simulations. Solvation is simulated in SCFT by constraining the glassy membrane matrix while relaxing the brush-like membrane pore coating against the solvent. The kMC simulations capture the resulting solute spatial distribution and concentration-dependent local diffusivity in the polymer-coated pores.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Joshua T. Berryman, Amirhossein Taghavi, Florian Mazur, Alexandre Tkatchenko
Summary: To improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. The study finds that classical DNA models have excessive stiffness when it comes to stretching, which is not confirmed by experimental studies. Quantum correction provides a better explanation for the discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. This research is important for nucleic acid simulations and biomolecular simulations in general.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biophysics
Wylie Stroberg, Santiago Schnell
Summary: In this study, an algorithm was developed to simulate reversible reactions between reacting Brownian particles, investigating the effect of macromolecular crowding on reaction rates and correlation times for ligand-receptor systems. It was found that crowding could increase the accuracy of estimated ligand concentration based on receptor occupancy, particularly by enhancing the effective association rates between small ligands and receptors. Crowding also decreased the accuracy of receptor's estimate for larger ligands by decreasing the microscopic association and dissociation rates.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Physical
Estefania Diaz Lopez, Aleix Comas-Vives
Summary: This study evaluated Rh(111)-catalyzed dry reforming of methane (DRM) using density functional theory and kinetic Monte Carlo simulations. The results showed that the catalytic system displayed Arrhenius behavior with CO2 activation identified as the dominant step.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Physical
Xuan Tang, Wei Han
Summary: This study develops a multiscale approach to explore the pathways and kinetics of peptide aggregation nucleation. The research reveals a two-step mechanism for A beta(16-21) amyloid nucleation, and an unexpected atypical mechanism at submillimolar concentrations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Engineering, Mechanical
Sankhadeep Bhattacharyya, Md Rushdie Ibne Islam, Puneet Kumar Patra
Summary: This manuscript investigates the fracture crack propagation in graphene sheets using a sequential multiscaling technique. By coupling continuum-scale smoothed particle hydrodynamics (SPH) with atomistic scale molecular dynamics (MD) simulations through proper constitutive modelling, the authors accurately reproduce the atomistic scale stress-strain behavior until failure. The study reveals the influence of notch orientation on crack propagation and the changes in stress-strain behavior caused by randomly oriented cracks in graphene sheets.
THEORETICAL AND APPLIED FRACTURE MECHANICS
(2022)
Article
Biochemistry & Molecular Biology
Xiaowei Wang, Ilona Christy Unarta, Peter Pak-Hang Cheung, Xuhui Huang
Summary: This article introduces a protocol specifically tailored for studying functional conformational changes of proteins, emphasizing the importance of selecting proper molecular features to describe the slowest timescales of interest. The recommendation of spectral oASIS and deep learning methods for automatic feature selection and discovering collective variables is provided. Through case studies on DNA repair enzymes and RNA polymerases, recent applications of MSMs in elucidating molecular mechanisms of functional conformational changes are reviewed, along with discussions on the challenges and future prospects in constructing MSMs for studying protein conformational changes.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Mechanics
Claire Albrecht, Irene J. Beyerlein, Morgan R. Jones
Summary: In this work, a three-dimensional phase field-based formulation is presented for simulating the temperature-dependent motion of discrete dislocations in crystals. The method is applied to study pyramidal-type dislocations in three exemplar hexagonal close packed materials, Mg, Ti, and Zr. The results show that pyramidal slip is glissile and the activation stress and stacking fault widths are asymmetric with respect to forward/backward glide. The analysis also reveals the role of temperature in Frank-Read source operation and identifies a master inverse relationship for the dislocation loop nucleation rate with homologous temperature in all three materials.
EUROPEAN JOURNAL OF MECHANICS A-SOLIDS
(2023)
Article
Biochemistry & Molecular Biology
Miroslav Krepl, Tom Dendooven, Ben F. Luisi, Jiri Sponer
Summary: Hfq is a conserved protein involved in RNA-mediated gene expression control in bacteria. Molecular dynamics simulations revealed the extensive dynamics of the Hfq-RNA interface, providing insights into the assembly of the translation-repression complex. Dynamic substrate recognition by Hfq-RNA binding offers a structural rationale for the stepwise assembly of multicomponent ribonucleoprotein complexes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Alessandro Berselli, Fabio Benfenati, Luca Maragliano, Giulio Alberini
Summary: Claudins (Cldns) are transmembrane proteins that play a major role in tight junction integrity and tissue selectivity. Computational methodologies have been used to investigate the properties of Cldn and provide valuable insights for improving the characterization of Cldn and designing strategies for controlling paracellular transport.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Alessandro Berselli, Fabio Benfenati, Luca Maragliano, Giulio Alberini
Summary: Claudins are transmembrane proteins that play a crucial role in tight junction integrity and tissue selectivity. They form barriers or ion-selective channels between cells in the paracellular space. Computational methodologies have helped to elucidate the properties of Claudins and could be useful for designing strategies to control the transport of drugs or molecules.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Kelly E. Du Pont, Russell B. Davidson, Martin McCullagh, Brian J. Geiss
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Chemistry, Physical
Ryan Weber, Martin McCullagh
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Nanoscience & Nanotechnology
Si Wu, Eunkyoung Kim, Chen-yu Chen, Jinyang Li, Eric VanArsdale, Christopher Grieco, Bern Kohler, William E. Bentley, Xiaowen Shi, Gregory F. Payne
ADVANCED ELECTRONIC MATERIALS
(2020)
Article
Chemistry, Physical
Forrest R. Kohl, Yuyuan Zhang, Aaron P. Charnay, Lara Martinez-Fernandez, Bern Kohler
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Chemistry, Physical
Yuyuan Zhang, Chen He, Jeffrey T. Petty, Bern Kohler
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Multidisciplinary Sciences
Christopher Grieco, Forrest R. Kohl, Alex T. Hanes, Bern Kohler
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Physical
Yuyuan Zhang, Chen He, Kimberly de la Harpe, Peter M. Goodwin, Jeffrey T. Petty, Bern Kohler
Summary: The specific nucleobase subunits within a DNA strand modulate cluster-ligand interactions and brightness, with guanosine and inosine affecting the fluorescence brightness and decay rate differently. Nonradiative decay is 7x higher with guanosine than inosine, indicating a potential correlation between nonradiative decay and selective coordination with specific nucleobase subunits.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Jennifer M. Empey, Christopher Grieco, Natasha W. Pettinger, Bern Kohler
Summary: The study reveals that electrons are injected into trap or defect states with Ce 5d character in CeO2 nanoparticles following photoexcitation of dye molecules. The decay of electrons in the oxidized dye is slightly slower than the mid-IR signals, indicating competition between electron relaxation within CeO2 and back-electron transfer to the dye. These results provide insights into elementary events crucial for understanding photocatalysis with CeO2 nanoparticles.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Physical
Alex T. T. Hanes, Christopher Grieco, Remy F. F. Lalisse, Christopher M. M. Hadad, Bern Kohler
Summary: Two-dimensional infrared (2D IR) spectroscopy, infrared pump-infrared probe spectroscopy, and density functional theory calculations were used to investigate vibrational relaxation in methylated xanthine derivatives. The results showed biexponential decay of carbonyl stretch modes and a quantum beat in anisotropy signals. Coherent energy transfer and intramolecular vibrational redistribution were observed. The decay of ring modes was explained by intermolecular energy transfer to solvent modes. The coupling between carbonyl stretching modes and ring modes was found to be weak.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Xueqing Wang, Lilia Kinziabulatova, Marco Bortoli, Anju Manickoth, Marisa A. Barilla, Haiyan Huang, Lluis Blancafort, Bern Kohler, Jean-Philip Lumb
Summary: Melanins are biopolymers produced from phenols and catechols that provide various functions such as photoprotection, pigmentation, and redox activity. The chemical structures of melanins remain unknown, hindering the design of synthetic materials with specific properties. However, the stabilization of indole-5,6-quinone (IQ) derivatives has allowed the exploration of eumelanin's unique electronic and optical properties, which can contribute to the development of melanin-inspired materials.
Article
Chemistry, Multidisciplinary
Zhiling Zhao, Eunkyoung Kim, Chen-Yu Chen, John R. Rzasa, Qian Zhang, Jinyang Li, Yang Tao, William E. Bentley, Jean-Philip Lumb, Bern Kohler, Gregory F. Payne
Summary: Catechol-based materials in redox-based bioelectronics possess diverse properties and can transduce near infrared (NIR) radiation into heat. The study shows that catechol-chitosan films can reversibly respond to both NIR and redox inputs, suggesting the independent flow of energy through catechol-based materials via redox and electromagnetic modalities. These findings highlight the potential of catecholic materials for bio-device communication, offering both short-range redox communication and long-range electromagnetic communication.
MATERIALS CHEMISTRY FRONTIERS
(2022)
Article
Chemistry, Physical
Natasha W. Pettinger, Jennifer M. Empey, Sascha Frobel, Bern Kohler
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
Article
Chemistry, Multidisciplinary
Forrest R. Kohl, Christopher Grieco, Bern Kohler
Article
Chemistry, Physical
Christopher Grieco, Jennifer M. Empey, Forrest R. Kohl, Bern Kohler
FARADAY DISCUSSIONS
(2019)
Article
Chemistry, Multidisciplinary
Yuyuan Zhang, Kimberly De la Harpe, Forrest R. Kohl, Bern Kohler
CHEMICAL COMMUNICATIONS
(2019)