Article
Physics, Applied
Elham Sharafedini, Hossein Hamzehpour, Mohammad Alidoust
Summary: We have developed a method to study the charge conductivity of a porous system or a metallic matrix alloyed by randomly distributed nonmetallic grains and vacancies. By incorporating Schrodinger's equation and Poisson's equation, we used Monte Carlo sampling to generate random alloys and statistically evaluate the charge conductance. Our parametric study revealed that the charge conductance shows highly nonlinear behavior in the low-voltage regime due to quantum scattering processes, while it remains constant in the high-voltage regime. These findings provide valuable insights for future experiments in designing circuital elements involving random alloy systems.
JOURNAL OF APPLIED PHYSICS
(2023)
Article
Biochemical Research Methods
Dillion M. Fox, Christopher M. MacDermaid, Andrea M. A. Schreij, Magdalena Zwierzyna, Ross C. Walker
Summary: RNA folding is a complex computational problem, and this study explores using quantum computing hardware to predict the secondary structure of RNA. It demonstrates the competitiveness of quantum annealers in finding low energy solutions.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Alexandre S. Avaro, Juan G. Santiago
Summary: This article presents a quantification of the uncertainty in the experimental determination of kinetic rate parameters for enzymatic reactions. The authors examine several sources of uncertainty and bias and compute typical uncertainties of kcat, KM, and catalytic efficiency. The extraction of these parameters for CRISPR-Cas systems is analyzed as a salient example. Reports of enzymatic kinetic rates for CRISPR diagnostics have been highly unreliable and inconsistent.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Quantum Science & Technology
Carsten Blank, Daniel K. Park, Francesco Petruccione
Summary: Discrete stochastic processes (DSP) are widely used in modeling the dynamics of probabilistic systems, often analyzed using Monte-Carlo methods. A quantum algorithm for calculating the characteristic function of a DSP has been proposed, which grows linearly with the number of time steps and guarantees optimal variance without the need for importance sampling.
NPJ QUANTUM INFORMATION
(2021)
Article
Operations Research & Management Science
Yi Chen, Jing Dong, Hao Ni
Summary: The article introduces an algorithm for simulating fractional Brownian motion, supporting user-specified error bounds and providing different error guarantees for different Hurst indices. Building on this, the algorithm is extended to simulate stochastic differential equations driven by fBM, allowing for efficient estimation of function expectations.
MATHEMATICS OF OPERATIONS RESEARCH
(2021)
Article
Physics, Fluids & Plasmas
Vladimir P. Zhdanov
Summary: Chemisorption can cause reshaping of metal nanocrystallites with surface tension dependent on adsorbate coverage. Disagreement exists on how to calculate surface tension in this case. Statistical physics laws clarify that surface tension can be described uniformly under different adsorption scenarios.
Article
Engineering, Electrical & Electronic
A. A. Spirina, N. L. Shwartz
Summary: The high-temperature GaAs annealing kinetics were studied through Monte Carlo simulation. It was found that the surface morphology evolution and evaporation kinetics are dependent on the GaAs substrate orientation. Different evaporation modes on different surface orientations result in variations in the evaporation rate.
MATERIALS SCIENCE IN SEMICONDUCTOR PROCESSING
(2021)
Article
Robotics
Peng Xu, Liang Ding, Zhikai Wang, Haibo Gao, Ruyi Zhou, Zhaopei Gong, Guangjun Liu
Summary: This letter proposes a novel coordinative planning method for hexapod robots, treating gait and foothold planning as a sequence optimization problem. By considering the environment's harshness as the leg's fault and using the Monte Carlo tree search algorithm, the method effectively improves the passability of the hexapod robot in challenging terrains with sparse footholds.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2022)
Article
Mechanics
Haibing Peng
Summary: Despite the widespread use of Navier-Stokes equations in computational-fluid-dynamics (CFD), there are still unanswered questions due to the absence of considering the statistical nature of discrete air molecules. In this study, we propose a statistical mechanics-based approach called the volume-element method, which allows for the numerical evaluation of aerodynamic lift and drag. We obtained pressure and friction values as a function of the angle of attack for flat-plate airfoils, and this method can be directly applied to convex-shape airfoils and combined with Monte Carlo simulations for concave-shape airfoils. This approach not only has implications for aerodynamic applications, but also opens up possibilities for further applications in Boson or Fermi gases.
Article
Mechanics
Hao Yang, Jun Zhang
Summary: In this study, a new theoretical framework for the information preservation (IP) method based on kinetic theory is introduced to offer a complete understanding of the preserved information's transport properties. By introducing a velocity-information joint distribution function (VIJDF) and deriving its governing equation as well as the corresponding macroscopic transport equations, the accuracy of the IP method is ensured. Numerical simulations demonstrate that the IP method can achieve similar accuracy as the DSMC method with a much smaller sampling size.
Article
Materials Science, Multidisciplinary
Chao Jiang, Yongfeng Zhang, Larry K. Aagesen, Andrea M. Jokisaari, Cheng Sun, Jian Gan
Summary: Understanding the interactions of noble gases with metals is crucial for designing radiation-resistant structural materials for nuclear reactors. A unified theory has been proposed to describe the energetics of noble gas bubbles in various bcc metals, revealing the exceptional thermal stability of Ne, Ar, and Kr bubbles compared to He bubbles. The study provides new insights on the stability of fission gas bubble superlattice in bcc U-Mo and shows good agreement with existing thermal helium desorption spectrometry experiments.
Article
Physics, Multidisciplinary
K. L. Zhang, Z. Song
Summary: The study reveals that applying a nonlocal non-Hermitian perturbation to an Ising chain merges the topological Kramer-like degeneracy in the ferromagnetic phase, with distinct dynamic responses for different quantum phases. The phase diagram at zero temperature is completely preserved at finite temperatures.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Kang Wang, Yunan He, Yu Shen, Yan Wang, Xiaojun Xu, Xiaohui Song, Tingting Sun
Summary: This paper investigates the importance of pausing events in RNA cotranscriptional folding and reveals that they play a critical role in cellular RNA function. The findings show that pausing events generate valid cotranscriptional conformational rearrangement to protect function structures, influencing the folding pathway. Different transcription speeds result in varying levels of protection capability. The folding pathway can also be affected by a change in transcription speed after a pausing site. These findings highlight the complex rearrangement folding in pausing events and the preference of different RNAs for specific folding pathways. Pausing can be employed to regulate the population of final functional structures.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Optics
Ruoyu Chen, Shanbao Tong, Peng Miao
Summary: This study proposes a deep-learning-based strategy for high spatiotemporal resolution three-dimensional (3D) reconstruction from a single transilluminated laser speckle contrast image, providing more structural and functional details without multifocus two-dimensional (2D) imaging or 3D optical imaging with point/line scanning. The method utilizes convolution of vessel masks with depth-dependent point spread functions (PSF) to generate a large training dataset, and employs UNet and ResNet for deblurring and depth estimation. The blood flow in the reconstructed 3D vessels is estimated by a depth-dependent contrast model. The proposed method achieves high-fidelity structural reconstruction with a depth-independent estimation of blood flow, and is suitable for real-time monitoring of thick tissue and the diagnosis of vascular diseases.
Article
Chemistry, Physical
Shiyan Wang, Anirudh Venkatesh, Doraiswami Ramkrishna, Vivek Narsimhan
Summary: A Brownian bridge is a continuous random walk guided by an effective drift to control the endpoint of a stochastic process. While widely applicable in chemical science, the main limitation is the difficulty in determining the effective drift and solving the complex Backward Fokker-Planck equation.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Yifan Zhang, Sambuddha Sen, David P. Giedroc
Article
Biochemistry & Molecular Biology
Abhinaba Ray, Katherine A. Edmonds, Lauren D. Palmer, Eric P. Skaar, David P. Giedroc
Article
Biophysics
Katherine A. Edmonds, Yifan Zhang, Daniel J. Raines, Anne-K Duhme-Klair, David P. Giedroc
BIOMOLECULAR NMR ASSIGNMENTS
(2020)
Article
Microbiology
Reece J. Knippel, Aaron G. Wexler, Jeanette M. Miller, William N. Beavers, Andy Weiss, Valerie de Crecy-Lagard, Katherine A. Edmonds, David P. Giedroc, Eric P. Skaar
CELL HOST & MICROBE
(2020)
Review
Microbiology
Matthew R. Jordan, Jiefei Wang, Daiana A. Capdevila, David P. Giedroc
CURRENT OPINION IN MICROBIOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Brenna J. C. Walsh, David P. Giedroc
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Daiana A. Capdevila, Brenna J. C. Walsh, Yifan Zhang, Christopher Dietrich, Giovanni Gonzalez-Gutierrez, David P. Giedroc
Summary: Structural and kinetic analyses of the transcriptional repressor protein SqrR reveal its persulfide selectivity mechanism, shedding light on the coordinated regulation function of cysteine thiol-based transcriptional regulators in cellular redox homeostasis.
NATURE CHEMICAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Giuliano T. Antelo, Alejandro J. Vila, David P. Giedroc, Daiana A. Capdevila
Summary: The molecular evolution of the adaptive response at the host-pathogen interface, known as an 'arms race,' involves strategies employed by the innate immune system to starve microbes of metals, countered by pathogens maintaining access to metal ions. Recent exploration of how evolution repurposes host and pathogen proteins to perform new functions is discussed, with a focus on metalloproteins restricting bacterial access to transition metals. Coevolution with bacterial metal acquisition systems and the evolution of metallo-?-lactamases in the context of host-imposed nutritional immunity are also examined.
TRENDS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Joseph N. Fakhoury, Yifan Zhang, Katherine A. Edmonds, Mauro Bringas, Justin L. Luebke, Giovanni Gonzalez-Gutierrez, Daiana A. Capdevila, David P. Giedroc
Summary: CstR is a protein that senses persulfides and regulates bacterial response to hydrogen sulfide and other oxidized reactive sulfur species. Research suggests that the specificity of CstRs to different oxidants is determined by their sequence, structural, and kinetic features.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Andy Weiss, Caitlin C. Murdoch, Katherine A. Edmonds, Matthew R. Jordan, Andrew J. Monteith, Yasiru R. Perera, Aslin M. Rodriguez Nassif, Amber M. Petoletti, William N. Beavers, Matthew J. Munneke, Sydney L. Drury, Evan S. Krystofiak, Kishore Thalluri, Hongwei Wu, Angela R. S. Kruse, Richard D. DiMarchi, Richard M. Caprioli, Jeffrey M. Spraggins, Walter J. Chazin, David P. Giedroc, Eric P. Skaar
Summary: This study reveals the existence of a conserved COG0523 protein family in vertebrates and assigns them an important role in regulating cellular zinc homeostasis.
Article
Microbiology
Erin R. Green, Joseph N. Fakhoury, Andrew J. Monteith, Hualiang Pi, David P. Giedroc, Eric P. Skaar
Summary: This study reveals that Acinetobacter baumannii causes more virulent pneumonia following desiccation and identifies the genetic requirements for desiccation. The disruption of Lon protease enhances desiccation tolerance, while bacterial hydrophilins DtpA and DtpB play a crucial role in this process.
CELL HOST & MICROBE
(2022)
Article
Biochemistry & Molecular Biology
Yifan Zhang, Julia E. Martin, Katherine A. Edmonds, Malcolm E. Winkler, David P. Giedroc
Summary: The novel virulence associated Rrf2-family transcriptional repressor SifR regulates genes involved in iron uptake and stress response in Streptococcus pneumoniae, providing insight into how the bacterium acquires iron sources in the host environment. This study sheds light on the mechanisms by which the pathogen adapts to oxidative stress and utilizes catechol-derived iron sources for survival.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Brenna J. C. Walsh, Sofia Soares Costa, Katherine A. Edmonds, Jonathan C. Trinidad, Federico M. Issoglio, Jose A. Brito, David P. Giedroc
Summary: Hydrogen sulfide (H2S) is a cytoprotective agent used by bacteria in response to stress, and this study found that exogenous sulfide alters protein abundance and metabolic reactions in the gut microorganism Enterococcus faecalis, potentially affecting fatty acid pathways.
Article
Biochemistry & Molecular Biology
Katherine A. Edmonds, Matthew R. Jordan, David P. Giedroc
Summary: This study uses genomic enzymology tools to analyze over 80,000 sequences related to zinc metallochaperones, revealing multiple distinct clusters including characterized and uncharacterized COG0523 proteins. Through the analysis of these clusters, new perspectives on COG0523 proteins as cellular reporters of nutrient stress induced by zinc limitation are discussed.
Article
Biology
Brenna J. C. Walsh, David P. Giedroc
Summary: Hydrogen sulfide has been found to play a crucial role in bacterial cytoprotection against host immune response, possibly through the formation of reactive sulfur species derived from H2S. A new analytical method has been developed and successfully applied to studying protein persulfidation in bacterial cells, particularly in a major human pathogen. This method allows quantification and identification of persulfidation sites in the proteome, which may serve as regulatory modifications that can be validated through biochemical studies.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)