Article
Physics, Fluids & Plasmas
Vikash Pandey
Summary: Most materials exhibit creep memory under constant load. The memory behavior is governed by Andrade's creep law, which also has a connection with earthquake aftershocks. The physical interpretation of these empirical laws is lacking, and attempts to use fractional derivatives lack confidence. In this study, a linear physical mechanism is established to explain both laws and relate the parameters to the material's macroscopic properties.
Article
Computer Science, Theory & Methods
Amish Goel, Pierre Moulin
Summary: This paper proposes a locally-optimal generalized likelihood ratio test (LO-GLRT) for detecting targeted attacks on a classifier, which involves adding a norm-bounded targeted universal adversarial perturbation (UAP) to the classifier's input. The paper analyzes and evaluates the test, finding it to be effective in detecting the attacks.
IEEE TRANSACTIONS ON INFORMATION FORENSICS AND SECURITY
(2022)
Article
Chemistry, Physical
Vitali Tugarinov, Alberto Ceccon, G. Marius Clore
Summary: The dynamics of methyl-bearing side chains in proteins were investigated through C-13 relaxation measurements, revealing correlations and anticorrelations between parameters, which can be partially decorrelated through the analysis of different C-13 magnetization modes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biology
Ashwin Balakrishnan, Katherina Hemmen, Susobhan Choudhury, Jan-Hagen Krohn, Kerstin Jansen, Mike Friedrich, Gerti Beliu, Markus Sauer, Martin J. Lohse, Katrin G. Heinze
Summary: The study explores the mobility of the beta 2-adrenergic receptor over a wide temporal range, from nanoseconds to seconds, using various fluorescence spectroscopy techniques. It reveals both translational and rotational mobility, which were previously hidden or overlooked, providing a comprehensive understanding of the receptor's dynamics.
COMMUNICATIONS BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Samantha A. Miles, Joshua Andrew Nillama, Luke Hunter
Summary: This review summarizes the applications of side chain-fluorinated amino acids in medicinal chemistry and protein science. The paper outlines strategies for incorporating fluorine atoms into amino acid side chains and elaborating these building blocks into more complex fluorinated peptides and proteins. It then describes the diverse benefits of fluorine in amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
Article
Chemistry, Physical
Srijit Mukherjee, Premashis Manna, Nancy Douglas, Prem P. Chapagain, Ralph Jimenez
Summary: The higher brightness of mCherry-XL compared to mCherry is due to a decrease in its nonradiative decay rate. Molecular dynamics simulations revealed that the I197R mutation increases the rigidity of the beta-barrel. The simulations also showed steric interactions and hydrogen bonding interactions critical for perturbing the chromophore electronic structure.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Physics, Fluids & Plasmas
Syed Shuja Hasan Zaidi, Prabhat K. Jaiswal, Madhu Priya, Sanjay Puri
Summary: Simulation results from a molecular dynamics study on surface-directed spinodal decomposition at wetting surfaces are presented. The study investigates the wetting kinetics in the early stage using long-ranged and short-ranged surface fields. It is found that the wetting-layer thickness exhibits power-law growth at very early times and then transitions to a fast-mode regime. Interestingly, a similar rapid growth is observed for the short-ranged surface potential as well.
Article
Chemistry, Multidisciplinary
Morgane Callon, Dominique Luder, Alexander A. Malaer, Thomas Wiegand, Vaclav Rimal, Lauriane Lecoq, Anja Boeckmann, Ago Samoson, Beat H. Meier
Summary: NMR spectra of side-chain protons in proteins provide important information about their structure, dynamics, and mechanisms that regulate interactions between macromolecules. This study shows that combining a magic-angle-spinning (MAS) frequency of 160 kHz with a high magnetic field of 1200 MHz significantly improves the spectral resolution of these resonances. Detailed investigations on model samples and the hepatitis B viral capsid demonstrate the improved resolution of the side-chain region, enabling the assignment of aliphatic protons and opening up new possibilities for structural studies and characterization of protein-protein or protein-nucleic acid interactions.
Article
Chemistry, Multidisciplinary
Morgane Callon, Dominique Luder, Alexander A. Malaer, Thomas Wiegand, Vaclav Rimal, Lauriane Lecoq, Anja Boeckmann, Ago Samoson, Beat H. Meier
Summary: Magic-angle-spinning (MAS) frequencies and high magnetic field significantly improve the spectral resolution of side-chain protons in proteins, enabling better study of protein structure and interactions.
Article
Neurosciences
Benjamin Mathieu, Antonin Abillama, Malvina Martinez, Laurence Mouchnino, Jean Blouin
Summary: Previous studies have shown that the sensory modality used to identify regions of the body hidden from sight, but frequently viewed, influences the type of the body representation employed for reaching them with the finger. This study aimed to investigate if this observation also applies to rarely viewed body regions. The results suggest that the position of rarely viewed body parts are spatially encoded by an exteroceptive body representation and that non-visual sensorimotor processes are involved in the constructing of this representation.
NEUROSCIENCE LETTERS
(2022)
Article
Multidisciplinary Sciences
Akito Noiri, Kenta Takeda, Takashi Nakajima, Takashi Kobayashi, Amir Sammak, Giordano Scappucci, Seigo Tarucha
Summary: Fault-tolerant quantum computers rely on quantum error correction, and the surface code is one of the most promising error correction codes. However, only a few qubit platforms have met the required gate fidelities. In this study, the researchers demonstrate high-fidelity gate operations in silicon spin qubits using fast electrical control and a micromagnet-induced gradient field. The results show a two-qubit gate fidelity of 99.5% and single-qubit gate fidelities of 99.8%, surpassing the fault-tolerance threshold for universal gates.
Article
Computer Science, Artificial Intelligence
Jiazhu Dai, Le Shu
Summary: An optimized algorithm based on the orientations of perturbation vectors is proposed to enhance the performance of generating universal perturbations in CNN models. Experimental results show that the proposed algorithm can generate universal perturbations in a shorter time with a higher fooling-rate increment in both white-box and black-box attacks compared to the original algorithm.
Editorial Material
Microbiology
Stefano G. Giulieri
Summary: Acquiring PBP2a is crucial for Staphylococcus aureus to develop resistance to beta-lactam antibiotics. While mec gene can be easily identified using PCR assays, these tools are not effective in detecting mec-independent oxacillin resistance. This study highlights the diagnostic and therapeutic challenges in managing mec-independent oxacillin resistance.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Chemistry, Physical
Nicolas Bolik-Coulon, Fabien Ferrage
Summary: Nuclear Magnetic Resonance (NMR) is a useful tool for studying molecular motions. The Model-Free (MF) approach has been widely used to analyze NMR relaxation rates, but complementing it with molecular dynamics (MD) simulations is necessary to obtain a mechanistic understanding of the motions. This paper demonstrates how to build explicit models of methyl-bearing protein side chain motions and compares them with the MF approach.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Mechanics
Young Dal Jeong, Min Je Kim, Jae Hwa Lee
Summary: Numerical simulations are conducted to explore the intermittent swimming gait of fish schools using two self-propelled flexible fins. Different tail-beating modes, including HT, MTS, and MTL modes, are applied to investigate their effects on lateral gap distances and cost of transport (COT). The results show that MTL mode achieves a stable state with a small lateral gap distance, leading to a smaller COT compared to CT mode.
JOURNAL OF FLUID MECHANICS
(2023)
Article
Biophysics
Rajitha T. Rajeshwar, Andriy Anishkin, Sergei Sukharev, Juan M. Vanegas
Summary: Membrane tension perceived by mechanosensitive proteins mediates cellular responses to mechanical stimuli and guides various biological functions. A novel locally distributed tension molecular dynamics (LDT-MD) simulation method successfully reproduces and reversibly transitions MscL to the open state, allowing exploration of the MscL-gating process.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Christopher M. Topham, Jeremy C. Smith
Summary: The study investigates the binding interactions between the E-base and thymine and uracil bases, finding significant strain energy in systems containing a beta-alanine linker, while the E-base swings away from the target bases into the solvent in systems containing a 3-trans olefin linker. Additionally, calculations on a novel 2-cis olefin linker design suggest potential simultaneous hydrogen bonding with the thymine 4-oxo group, circumvention of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Chemistry, Physical
Laura Zanetti-Polzi, Micholas Dean Smith, Chris Chipot, James C. Gumbart, Diane L. Lynch, Anna Pavlova, Jeremy C. Smith, Isabella Daidone
Summary: The catalytic reaction in the SARS-CoV-2 main protease is activated by a proton transfer, with inhibitors reducing the free energy cost to reach the charge-separated state of the active-site dyad. Specific water molecules play a crucial role in enhancing or reducing the thermodynamic feasibility of the proton transfer reaction.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Rajitha T. Rajeshwar, Moumita Saharay, Jeremy C. Smith, Marimuthu Krishnan
Summary: The study focuses on the fast side-chain dynamics and conformational entropy changes during protein binding, demonstrating that significant flexibility changes are unlikely after ligand binding and establishing a linear correlation between O-axis(2) and conformational entropy changes for protein-ligand complexes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Medicinal
Bhagyesh Varvdekar, Akshay Prabhakant, Marimuthu Krishnan
Summary: Terahertz protein vibrations are sensitive reporters of protein structure and interactions. The study highlights the significant role of protein-ligand and solvent interactions in modulating low-frequency protein vibrations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Sree Kavya Penneru, Moumita Saharay, Marimuthu Krishnan
Summary: Bacterial cellulase enzymes are potential candidates for the efficient production of bioethanol from cellulosic biomass. CelS is a microbial enzyme that cleaves cellulose into cellobiose. This study investigates the mechanism of substrate dynamics and product expulsion in CelS through molecular dynamics simulations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Shaunak Badani, Marimuthu Krishnan
Summary: RENS is a computational technique that achieves extensive configurational sampling from a sequence of equilibrium and nonequilibrium MD simulations without modifying the potential energy surface. Unlike REMD, RENS uses nonequilibrium heating and cooling simulations to improve acceptance probability with only a few replicas.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Viswanathan Gurumoorthy, Utsab R. Shrestha, Qiu Zhang, Sai Venkatesh Pingali, Eric T. Boder, Volker S. Urban, Jeremy C. Smith, Loukas Petridis, Hugh O'Neill
Summary: c-Src kinase is a non-receptor tyrosine kinase that phosphorylates signaling proteins in cancers. This study focuses on the N-terminal disordered region (SH4UD) and its interactions with other domains of c-Src kinase. The results show that the presence of SH4UD leads to structural changes in the regulatory domains (SH3-SH2), indicating the importance of the disordered region for allosteric interactions. This study provides insights that may aid in the development of therapeutic interventions targeting the regulatory domains of c-Src kinase.
Article
Chemistry, Multidisciplinary
Luoxi Tan, Haden L. Scott, Micholas Dean Smith, Sai Venkatesh Pingali, Hugh M. O'Neill, Jennifer L. Morrell-Falvey, John Katsaras, Jeremy C. Smith, Brian H. Davison, James G. Elkins, Jonathan D. Nickels
Summary: Biofuels are crucial for sustainable energy and optimizing their production is a societal and economic imperative. Reducing the toxicity of co-solvents can improve the efficiency of biofuel production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Physical
Mood Mohan, Micholas Dean Smith, Omar Demerdash, Michelle K. Kidder, Jeremy C. Smith
Summary: Understanding the physical properties of ionic liquids is crucial for various industrial and research applications, but experimental screening can be challenging and expensive. Previous research has shown that combining quantum-mechanics-based property prediction tools with machine learning approaches can help screen and design ionic liquids with desired properties. However, the most appropriate machine learning approach is still unclear.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Mood Mohan, Micholas Dean Smith, Omar N. Demerdash, Blake A. Simmons, Seema Singh, Michelle K. Kidder, Jeremy C. Smith
Summary: Ionic liquids (ILs) have unique solvent properties, but it is unrealistic to experimentally determine their physicochemical properties. To address this issue, we developed machine learning models to predict the surface tension and speed of sound of ILs, which showed excellent agreement with experimental observations. This study paves the way for the development of machine learning models for predicting IL properties.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Nikhil Jakhar, Akshay Prabhakant, Marimuthu Krishnan
Summary: UV radiation-induced DNA damages, particularly the cyclobutane pyrimidine dimer (CPD) lesions, have adverse effects on genome integrity and cellular function. Rad4/XPC protein is responsible for recognizing and repairing CPD lesions, but the molecular mechanism behind this process has been elusive. By using enhanced sampling and molecular dynamics simulations, this study investigates the mechanism and energetics of lesion recognition by Rad4/XPC. The findings shed light on the sequence of events and their potential coupling, providing important insights into understanding UV-related skin disorders and cancers and facilitating the development of novel therapeutic strategies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Medicinal
Rupesh Agarwal, T. Rajitha Rajeshwar, Jeremy C. Smith
Summary: Structure-based virtual high-throughput screening is commonly used in early-stage drug discovery. This study evaluated the performance of three docking protocols on 173 RNA-small molecule crystal structures. The results showed that Vina and rDock are both applicable for projects without known ligand-protein structures, but their performance is relatively poor compared to protein-target docking methods.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
