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Immunology
Neelakantan Thulasi Devika, Ashok Kumar Jangam, Vinaya Kumar Katneni, Prasanna Kumar Patil, Suganya Nathamuni, Mudagandur Shashi Shekhar
Summary: The study utilized constraint-based genome-scale metabolic modeling approach to screen and identify six candidate bacterial strains with growth enhancement and pathogen suppression capabilities, including three novel strains, for probiotic applications. This is the first study to apply genomic-scale metabolic models for aquaculture purposes and detect bacterial species limiting Vibrio harveyi growth.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
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Quantum Science & Technology
Matija Medvidovic, Giuseppe Carleo
Summary: In this study, a new method is introduced to simulate layered quantum circuits using a neural network parametrization, allowing for accurate Quantum Approximate Optimization Algorithm (QAOA) simulations with smaller computational resources.
NPJ QUANTUM INFORMATION
(2021)
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Chemistry, Analytical
Laura Pires da Mata Costa, Amanda L. T. Brandao, Jose Carlos Pinto
Summary: Polystyrene chemical recycling via pyrolysis is an appropriate method for post-consumption material disposal. However, there is a lack of modeling studies on the degradation mechanism. This study developed a detailed mechanistic model to understand the kinetics of polystyrene degradation and validated the model through experimental data.
JOURNAL OF ANALYTICAL AND APPLIED PYROLYSIS
(2022)
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Chemistry, Physical
Xiao Kong, Jianing Zhuang, Liyan Zhu, Feng Ding
Summary: This study presents a low computational cost large-scale kinetic Monte Carlo (KMC) algorithm to simulate the evolution of graphene islands during growth and etching processes, providing new insights and data for understanding the growth and etching of graphene.
NPJ COMPUTATIONAL MATERIALS
(2021)
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Biochemical Research Methods
Daniel R. Weilandt, Pierre Salvy, Maria Masid, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis
Summary: Large-scale kinetic models are essential for understanding the dynamic and adaptive responses of biological systems, but the lack of computational tools for building and analyzing these models has been a limitation. This study presents a Python package (SKiMpy) that bridges this gap by providing an efficient toolbox for generating and analyzing large-scale kinetic models in various biological domains. The toolbox also allows for efficient parameterization of kinetic models and implementation of multispecies bioreactor simulations.
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Biochemical Research Methods
Sanmitra Ghosh, Paul J. Birrell, Daniela De Angelis
Summary: In this paper, a computationally efficient method is proposed to quantify the uncertainty in transmission ability during an epidemic. This method does not make assumptions about the timing and magnitude of the impacts of external stimuli on transmission. The proposed approach is valuable for real-time monitoring of epidemics and has been demonstrated through examples of influenza, seasonality, and COVID-19 modeling.
PLOS COMPUTATIONAL BIOLOGY
(2023)
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Geosciences, Multidisciplinary
Alexander Schaaf, Miguel de la Varga, Florian Wellmann, Clare E. Bond
Summary: This paper introduces a method to incorporate geological information into probabilistic geomodeling using the open-source software GemPy. By checking simulated geomodel realizations against topology information without specifying a likelihood function, the method demonstrates the feasibility of constraining and improving probabilistic geomodel ensembles with reduced uncertainty.
GEOSCIENTIFIC MODEL DEVELOPMENT
(2021)
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Multidisciplinary Sciences
Yannik Schaelte, Jan Hasenauer
Summary: Calibrating model parameters on heterogeneous data can be challenging and inefficient. This paper proposes a method that combines scale normalization and regression-based summary statistics to improve efficiency and accuracy.
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Chemistry, Physical
Mehdi Ansari-Rad
Summary: The study uses kinetic Monte Carlo simulations to investigate the transport and annihilation of triplet excitons in organic phosphorescent host-guest systems. The results show that triplet transport in this system is dispersive during their lifetime under typical parameters, and a modified rate coefficient is proposed to explain the annihilation process. Valuable insights into the statistics of annihilation and efficiency roll-off are obtained through a probability density function analysis of triplet decay.
JOURNAL OF PHYSICAL CHEMISTRY C
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Biochemical Research Methods
Thomas Thorne, Paul D. W. Kirk, Heather A. Harrington
Summary: This article discusses the importance of inferring the parameters of models describing biological systems in reverse engineering and proposes a method combining topological data analysis with Approximate Bayesian Computation (ABC) to infer parameters in angiogenesis. The results demonstrate that this topological approach outperforms ABC methods using simpler spatial statistics. This is a first step towards a general framework for spatial parameter inference in biological systems.
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Physics, Multidisciplinary
Tom Westerhout, Mikhail I. Katsnelson, Andrey A. Bagrov
Summary: In this study, we focus on the real-valued signful ground-state wave functions of frustrated quantum spin systems. We demonstrate that the signs can be easily recovered from the amplitudes using an auxiliary classical Ising model. Our findings reveal the hidden simplicity of many-body sign structures.
COMMUNICATIONS PHYSICS
(2023)
Review
Chemistry, Multidisciplinary
Tommaso Casalini
Summary: The use of methods at molecular scale has led to the discovery of new active ligands and previously unknown binding sites. While molecular simulations can improve the design of drug delivery devices, their spatial resolution has limitations in capturing molecular-scale phenomena. Atomic scale simulations, acting as a computational microscope, shed light on the impact of molecular interactions on system behavior.
JOURNAL OF CONTROLLED RELEASE
(2021)
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.
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Biochemistry & Molecular Biology
Asher Moshe, Elya Wygoda, Noa Ecker, Gil Loewenthal, Oren Avram, Omer Israeli, Einat Hazkani-Covo, Itsik Pe'er, Tal Pupko
Summary: This study developed a probabilistic approach to infer genome rearrangement rate parameters and used an Approximate Bayesian Computation framework for inference. The method can help elucidate the role of genome rearrangement in evolution and simulate genomes with empirical dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Materials Science, Multidisciplinary
John A. Mitchell, Fadi Abdeljawad, Corbett Battaile, Cristina Garcia-Cardona, Elizabeth A. Holm, Eric R. Homer, Jon Madison, Theron M. Rodgers, Aidan P. Thompson, Veena Tikare, Ed Webb, Steven J. Plimpton
Summary: SPPARKS is an open-source simulation code that allows the development and running of various Monte Carlo models at the atomic or meso scales. It can be used to study solid-state materials and their dynamic evolution during processing. The code's modular nature allows the addition of new models and diagnostic computations without modifying its core functionality. It includes models for microstructural evolution, diffusion, thin film deposition, additive manufacturing, and can also implement grid-based algorithms.
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING
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Biochemical Research Methods
Radhakrishnan Mahadevan, Axel von Kamp, Steffen Klamt
Review
Biochemical Research Methods
Shyam Srinivasan, William R. Cluett, Radhakrishnan Mahadevan
BIOTECHNOLOGY JOURNAL
(2015)
Review
Biochemical Research Methods
Naveen Venayak, Nikolaos Anesiadis, William R. Cluett, Radhakrishnan Mahadevan
CURRENT OPINION IN BIOTECHNOLOGY
(2015)
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Cell Biology
M. Ahsanul Islam, Karsten Zengler, Elizabeth A. Edwards, Radhakrishnan Mahadevan, Gregory Stephanopoulos
INTEGRATIVE BIOLOGY
(2015)
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Cell Biology
Pratish Gawand, Fatumina Said Abukar, Naveen Venayak, Siavash Partow, Adilson E. Motter, Radhakrishnan Mahadevan
INTEGRATIVE BIOLOGY
(2015)
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Biotechnology & Applied Microbiology
Laurence Yang, Shyamsundhar Srinivasan, Radhakrishnan Mahadevan, William R. Cluett
METABOLIC ENGINEERING
(2015)
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Biotechnology & Applied Microbiology
Steffen Klamt, Radhakrishnan Mahadevan
METABOLIC ENGINEERING
(2015)
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Water Resources
G. D. Tartakovsky, A. M. Tartakovsky, T. D. Scheibe, Y. Fang, R. Mahadevan, D. R. Lovley
ADVANCES IN WATER RESOURCES
(2013)
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Biotechnology & Applied Microbiology
Nicholas Bourdakos, Enrico Marsili, Radhakrishnan Mahadevan
BIOTECHNOLOGY AND BIOENGINEERING
(2014)
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Biochemical Research Methods
Nadeera Jayasinghe, Ashley Franks, Kelly P. Nevin, Radhakrishnan Mahadevan
BIOTECHNOLOGY JOURNAL
(2014)
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Biotechnology & Applied Microbiology
Kai Zhuang, Laurence Yang, William R. Cluett, Radhakrishnan Mahadevan
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Geochemistry & Geophysics
Jiao Zhao, T. D. Scheibe, R. Mahadevan
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Multidisciplinary Sciences
M. Ahsanul Islam, Alison S. Waller, Laura A. Hug, Nicholas J. Provart, Elizabeth A. Edwards, Radhakrishnan Mahadevan
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Biotechnology & Applied Microbiology
Nicholas D. Gold, Christopher M. Gowen, Francois-Xavier Lussier, Sarat C. Cautha, Radhakrishnan Mahadevan, Vincent J. J. Martin
MICROBIAL CELL FACTORIES
(2015)