Article
Chemistry, Physical
Nicolai Kozlowski, Helmut Grubmuller
Summary: Markov state models are widely used to analyze protein dynamics, but lack of sufficient sampling for larger molecules like proteins leads to large uncertainties. In addition, there are other sources of uncertainty, such as choice of parameters and limited observations. This study quantified and ranked these uncertainties for small globular test proteins, revealing that insufficient sampling is the largest uncertainty and providing guidelines for required sampling accuracy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Medicinal
Rafael G. Viegas, Murilo N. Sanches, Alan A. A. Chen, Fernando V. Paulovich, Angel E. Garcia, Vitor B. P. Leite
Summary: Molecular dynamics (MD) simulations are powerful tools for studying the folding pathways of biomolecules. In this study, we used MD simulations to investigate the folding of an RNA tetraloop and analyzed the dynamics using the energy landscape visualization method (ELViM). Our results provide insights into the folding process of the tetraloop and demonstrate the potential of ELViM for studying biomolecules.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Nanoscience & Nanotechnology
Sehyun Doo, Ari Chae, Daesin Kim, Taegon Oh, Tae Yun Ko, Seon Joon Kim, Dong-Yeun Koh, Chong Min Koo
Summary: Understanding the oxidation reaction of aqueous Ti3C2Tx MXene suspensions is crucial for both academic studies and industrial applications. Comprehensive analysis revealed that the protonation of hydroxyl terminal groups under acidic conditions accelerates the oxidation reaction of titanium atoms, while the formation of bulky solvent cages under basic conditions retards their oxidative degradation.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Computer Science, Interdisciplinary Applications
Saurabh Shivpuje, Manish Kumawat, Abhijit Chatterjee
Summary: FT-TPMD is a new variation of the TPMD algorithm that allows for easier implementation of TPMD calculations and shows improvements in computational efficiency. It also has the capability for systematic detection of rare transition events, state classification, and rate constant calculation.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Wen-de Tian, Mohsen Ghasemi, Ronald G. Larson
Summary: The study utilized all-atom molecular dynamics simulations to extract the free energy of binding of potassium ions to charged poly(acrylic acid) chains, revealing that increasing the charge fraction of PAA led to more extended chain conformations and tighter potassium ion binding. The model used in the study provided semi-quantitative predictions for the binding free energy and degree of potassium binding to PAA chains as a function of PAA charge fraction without the need for fitting parameters.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Food Science & Technology
Ah-Na Kim, Oui Woung Kim, Hoon Kim
Summary: In this study, the temperature dependence of the physical, chemical, and sensory qualities of rice stored for 1 year at different temperatures was analyzed. It was found that seed viability had the highest temperature dependence, followed by germination rate, sensory characteristics, and fat acidity. The degradation rate increased and shelf life decreased logarithmically with temperature rise. Predictive equations for shelf life based on storage temperatures were developed.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Physical
Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks
Summary: The study introduces a machine learning method, GMVAE, which can perform dimensionality reduction and clustering of biomolecular conformations effectively. The model shows potential in analyzing the free energy landscape of protein folding, with highly separated clusters corresponding to metastable states during folding.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Physics, Multidisciplinary
P. Sarkanych, Yu. Holovatch, R. Kenna, T. Yavors'kii
Summary: The Fukui-Todo algorithm is an important simulational approach for tackling critical phenomena in statistical physics. The partition-function-zero approach is fundamental for understanding such phenomena and measuring their properties accurately. By using a novel reweighting technique and zero-detection protocol, the obstacles caused by bypassing sample-by-sample energy computation in the algorithm are overcome, demonstrating its efficacy in simple iconic models with transitions of both first and second order.
Article
Chemistry, Physical
Salma Sleiman, Jacques Huot
Summary: The study investigated the effects of particle size, pressure, and temperature on the first hydrogenation of TiVZrHfNb high entropy alloy. It was found that temperature had a significant impact on activation, while the influence of particle size was minor.
JOURNAL OF ALLOYS AND COMPOUNDS
(2021)
Article
Biochemistry & Molecular Biology
Bjarte Aarmo Lund, Bjorn Olav Brandsdal
Summary: A new method was developed to efficiently determine the temperature dependence of enzyme catalysis, requiring less sample, labor, and time. The method was validated with Bacillus pumilus LipA enzyme and three different enzymes, effectively differentiating between enzyme types at various temperatures.
Article
Chemistry, Physical
Ernesto Suarez, Rafal P. Wiewiora, Chris Wehmeyer, Frank Noe, John D. Chodera, Daniel M. Zuckerman
Summary: Markov state models (MSMs) are widely used in studying protein conformational dynamics, accurately reproducing correlation functions for states with longer lifetimes but facing stricter requirements for path-based observables; history-augmented MSMs (haMSMs) show more reliable performance in reproducing path-based observables, even in the presence of short-lived states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Mechanics
Fernando Takeshi Tanouye
Summary: We investigated the thermodynamic behavior of short HP-polymers on the square lattice and found a strong correlation between the occurrence of the heat capacity excitation peak at low temperatures and a sharp conformational gap.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2023)
Article
Food Science & Technology
Enjie Diao, Kun Ma, Hui Zhang, Peng Xie, Shiquan Qian, Huwei Song, Ruifeng Mao, Liming Zhang
Summary: Cysteine and temperature significantly affect the degradation efficiency of patulin in highly acidic conditions, with higher degradation rate constants and lower activation energy when cysteine is present. Increasing temperature clearly improves the degradation efficiency of patulin.
Article
Materials Science, Ceramics
Saibal Ray, Tapas Kumar Bhattacharya, Vivek Kumar Singh, Debabrata Deb, Shounak Ghosh, Santanu Das
Summary: Nanocrystalline calcium carbonate with varying particle sizes was successfully synthesized using precipitation techniques from an aqueous solution at controlled pH. The particle size and crystallite size could be precisely controlled by changing the precursor concentration, and the apparent activation energy of decomposition decreased with decreasing average particle size of nanocrystalline calcium carbonate.
CERAMICS INTERNATIONAL
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Hidenori Takeshima
Summary: This study aims to develop a fast and practical computation method for MR simulations. A new method is proposed to efficiently process subsequences with RF pulses by computing and managing combined transitions, which accelerates the simulation and makes it practical on a wide range of computers.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Article
Mathematical & Computational Biology
Stefanie Muff, Lukas F. Keller
BIOMETRICAL JOURNAL
(2015)
Article
Biodiversity Conservation
Irene C. Weinberger, Stefanie Muff, Addy de Jongh, Andreas Kranz, Fabio Bontadina
BIOLOGICAL CONSERVATION
(2016)
Article
Ecology
Stefanie Muff, Leonhard Held, Lukas F. Keller
METHODS IN ECOLOGY AND EVOLUTION
(2016)
Article
Nutrition & Dietetics
Einat A. Schmutz, Claudia S. Leeger-Aschmann, Thomas Radtke, Stefanie Muff, Tanja H. Kakebeeke, Annina E. Zysset, Nadine Messerli-Buergy, Kerstin Stuelb, Amar Arhab, Andrea H. Meyer, Simone Munsch, Jardena J. Puder, Oskar G. Jenni, Susi Kriemler
INTERNATIONAL JOURNAL OF BEHAVIORAL NUTRITION AND PHYSICAL ACTIVITY
(2017)
Article
Ecology
Benedikt Gehr, Elizabeth J. Hofer, Stefanie Muff, Andreas Ryser, Eric Vimercati, Kristina Vogt, Lukas F. Keller
Article
Health Care Sciences & Services
Stefanie Muff, Milo A. Puhan, Leonhard Held
STATISTICAL METHODS IN MEDICAL RESEARCH
(2018)
Article
Ecology
Christopher N. Kaiser-Bunbury, Stefanie Muff, Jane Memmott, Christine B. Mueller, Amedeo Caflisch
Article
Chemistry, Physical
S. Muff, A. Caflisch
JOURNAL OF CHEMICAL PHYSICS
(2009)
Article
Chemistry, Multidisciplinary
Michele Seeber, Angelo Felline, Francesco Raimondi, Stefanie Muff, Ran Friedman, Francesco Rao, Amedeo Caflisch, Francesca Fanelli
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2011)
Article
Chemistry, Physical
Sergei V. Krivov, Stefanie Muff, Arnedeo Caflisch, Martin Karplus
JOURNAL OF PHYSICAL CHEMISTRY B
(2008)
Article
Chemistry, Physical
Bo Qi, Stefanie Muff, Amedeo Caflisch, Aaron R. Dinner
JOURNAL OF PHYSICAL CHEMISTRY B
(2010)
Article
Statistics & Probability
Stefanie Muff, Andrea Riebler, Leonhard Held, Havard Rue, Philippe Saner
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS
(2015)
Article
Computer Science, Interdisciplinary Applications
Stefanie Muff, Manuela Ott, Julia Braun, Leonhard Held
COMPUTATIONAL STATISTICS & DATA ANALYSIS
(2017)
Article
Biochemistry & Molecular Biology
Stefanie Muff, Amedeo Caflisch
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2008)