Article
Physics, Multidisciplinary
Kohei Yoshimura, Sosuke Ito
Summary: The study generalizes the thermodynamic uncertainty relation and thermodynamic speed limit for deterministic chemical reaction networks, highlighting the role of the scaled diffusion coefficient derived from the connection between macro- and mesoscopic networks. The research shows that the product of the entropy production rate and the ratio of the scaled diffusion coefficient to the square of the rate of concentration change is bounded below by two, and states a trade-off relation between speed and thermodynamic quantities. These results are proven under the general setting of open and nonideal CRNs.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Chiyan Liu, Jian Liu, Yong Han, Zhangrui Wang, Hui Zhang, Xiaoming Xie, Bo Yang, Zhi Liu
Summary: The hydration process of a Nafion membrane was studied using ambient-pressure x-ray photoelectron spectroscopy (APXPS), which provided a quantitative analysis of water content and the transformation of sulfonic acid groups. The conductivity of the membrane was determined by electrochemical impedance spectroscopy, establishing a connection between the electrical properties and the microscopic mechanism. Ab initio molecular dynamics simulations provided core-level binding energies of O- and S-containing species in the Nafion + H2O system.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Medicine, Research & Experimental
Yujue Wang, Sheng Hui, Fredric E. Wondisford, Xiaoyang Su
Summary: Metabolic flux analysis aims to reveal metabolic reaction rates using stable isotope labeling patterns. The latest EMU framework expanded to simulate tandem mass spectrometry data has improved the precision of MFA. Combining MIDs of parent and daughter ions with TMID for MFA is more powerful than using TMID alone.
LABORATORY INVESTIGATION
(2021)
Article
Physics, Multidisciplinary
Kai Ueltzhoffer, Lancelot Da Costa, Daniela Cialfi, Karl Friston
Summary: Dissipative accounts of structure formation suggest that complex structures self-organize when they dissipate free energy that cannot be accessed otherwise, leading to a thermodynamic preference. However, the mechanisms underlying the selection of dissipative structures with thermodynamically efficient subprocesses are not fully understood, although research proposes a connection to bifurcation-based work-harvesting processes in the system.
Article
Biotechnology & Applied Microbiology
Tatsuya Sekiguchi, Hiroyuki Hamada, Masahiro Okamoto
Summary: Research has shifted from analyzing individual biochemical reactions to analyzing metabolic pathways as systems, which can be considered as characteristic multi-layered structures. The new version of WinBEST-KIT allows users to efficiently create and analyze multi-layered metabolic pathways, supporting SBML models.
BIOENGINEERING-BASEL
(2021)
Article
Physics, Multidisciplinary
J. Jara-Almonte, H. Ji
Summary: Through examining entropy production in fully kinetic simulations of collisional plasmas, it is shown that the transition from collisional Sweet-Parker reconnection to collisionless Hall reconnection can be viewed as a thermodynamic phase transition. A specific condition for the phase transition is identified, where the reconnection electric field satisfies a particular equation. During the phase transition, the heat capacity of the current sheet undergoes a discontinuous change, and a critical power law is observed in the effective heat capacity.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Jia-Ning Wang, Yuanfei Xue, Pengfei Li, Xiaoliang Pan, Meiting Wang, Yihan Shao, Yan Mo, Ye Mei
Summary: In silico investigations of enzymatic reactions and chemical reactions in condensed phases often require expensive computational resources due to the high number of degrees of freedom and large phase space. Reference-potential methods provide an alternative approach to achieve accurate simulations without significant loss of efficiency. This Perspective summarizes the concept of reference-potential methods, showcases recent applications, discusses pitfalls, and presents remedies.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Tomas Zimmermann, Filip Sebesta, Jaroslav Burda
Summary: This article highlights the importance of performing additional Legendre transformations in a constant pH environment for a correct thermodynamic description of reactions. The power of the new thermodynamic potential (ΔGA(0)) is demonstrated through three examples, showing its grand canonical character and pH dependency. The combination of this approach with QM/MM MD simulations also reveals interesting changes in energy values based on pH shifts.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Physics, Multidisciplinary
Alejandro P. Riascos, Francisco Hernandez Padilla
Summary: In this paper, a framework for comparing differences in occupation probabilities of two random walk processes on networks is presented. The framework considers modifications of the network or the transition probabilities between nodes. A dissimilarity measure is defined using the eigenvalues and eigenvectors of the normalized Laplacian. The framework is used to examine differences in diffusive dynamics, the effect of new edges and rewiring in networks, and divergences in transport in degree-biased random walks and random walks with stochastic reset.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Chemistry, Multidisciplinary
Xingyu Wang, Sanjubala Sahoo, Jose Gascon, Mikhail Bragin, Fangyuan Liu, Julia Olchowski, Samuel Rothfarb, Yuankai Huang, Wenjun Xiang, Pu-Xian Gao, S. Pamir Alpay, Baikun Li
Summary: In this study, the effects of polymer physical binding on the performance and selectivity of CO2RR were investigated. The addition of polytetrafluoroethylene (PTFE) was found to enhance the CO2 reduction process, modify the CO2RR pathway, and ultimately increase the average CH4 production by 10%. Despite an increase in ohmic resistance, the addition of PTFE lowered the energy barrier for CO protonation.
ENERGY & ENVIRONMENTAL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Lea Seep, Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Thermodynamic metabolic flux analysis (TMFA) can be utilized to narrow down the space of steady-state flux distributions, but requires knowledge of standard Gibbs free energy values. However, due to unknown ΔfG0 values of metabolites, a reaction lumping procedure has been proposed to eliminate these metabolites. The combined procedure proposed in this study efficiently identifies lumped reactions in genome-scale metabolic models and leads to more precise predictions compared to the original models when TMFA is applied.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Jie Gu
Summary: In this paper, we utilize the adiabatic approximation to study slow thermodynamic processes and derive the full counting statistics of work. We characterize the change in free energy and the dissipated work as dynamic-phase-like and geometric-phase-like quantities. The dynamic phase and geometric phase are linked to each other through the fluctuation-dissipation relation.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Tanmoy Biswas, A. de Oliveira Junior, Michal Horodecki, Kamil Korzekwa
Summary: This paper derives a version of the fluctuation-dissipation theorem within a resource-theoretic framework, providing a connection between the response of a system subject to perturbation and the fluctuations associated with observables in equilibrium. The results enable the optimal performance analysis of thermodynamic protocols for quantum states with coherence between different energy eigenstates.
Article
Biology
Dimitri Loutchko
Summary: The article explores the catalytic reaction system (CRS) formalism and demonstrates that it provides a natural setup to describe and analyze self-sustaining biochemical reaction networks. The CRS exhibits the algebraic structure of a semigroup with idempotent addition and a partial order, and can be represented as a discrete dynamical system on the power set of chemicals. The fixed points of this dynamical system correspond to self-sustaining sets of chemicals, with applications in characterizing maximal self-sustaining sets and functionally closed self-sustaining sets.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Physics, Multidisciplinary
Zhiyuan Jiang, You-Hui Su, Hongwei Yin
Summary: This study applies the method of information length to investigate the information change in linear and nonlinear biochemical reaction chains. The results show that the information does not always increase with the length of linear reaction chains, and the information in nonlinear reaction chains is influenced by the length, reaction coefficients, and rates.
Article
Neurosciences
Hamidreza Gharahi, C. Alberto Figueroa, Johnathan D. Tune, Daniel A. Beard
Summary: This study utilizes a multiscale modelling framework to investigate the metabolic mechanism(s) governing regional myocardial perfusion. The analysis identifies a maximally probable metabolic mechanism, which involves the proportional relationship between the production of a metabolic signalling factor and myocardial oxygen consumption, as well as the proportional relationship between oxygen delivery and flow.
JOURNAL OF PHYSIOLOGY-LONDON
(2022)
Article
Multidisciplinary Sciences
Homa MohammadiPeyhani, Jasmin Hafner, Anastasia Sveshnikova, Victor Viterbo, Vassily Hatzimanikatis
Summary: Metabolic dark matter refers to unknown metabolic processes that hinder our comprehensive understanding of metabolism and impede the development of biosynthetic cell factories and naturally derived pharmaceuticals. Utilizing computational solutions, this study successfully mapped known and unknown metabolic processes into a biochemical database containing 1.5 million biological compounds, predicting over 5 million reactions. The resulting ATLASx platform provides researchers with a powerful online tool for predicting and analyzing biochemical pathways.
NATURE COMMUNICATIONS
(2022)
Article
Biophysics
Daniel A. Beard, Bahador Marzban, On Yeung Li, Kenneth S. Campbell, Paul M. L. Janssen, Naomi C. Chesler, Anthony J. Baker
Summary: For patients with heart failure, the reduced ATP levels in the myocardium may impair the pump function of the failing heart, even though the reduction in ATP does not directly affect the function of contractile proteins.
BIOPHYSICAL JOURNAL
(2022)
Review
Biochemical Research Methods
Anastasia Sveshnikova, Homa MohammadiPeyhani, Vassily Hatzimanikatis
Summary: The metabolic engineering community relies on computational methods for pathway design in microbial hosts. Recent experimental research has highlighted new challenges and opportunities for computational pathway design. This review discusses the latest advances in computational discovery of new pathways and their potential for expanding metabolic capabilities, suggesting potential improvements for pathway design algorithms.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Anastasia Sveshnikova, Homa MohammadiPeyhani, Vassily Hatzimanikatis
Summary: This article presents a computational resource called ARBRE for predicting and ranking pathways to industrially important aromatic compounds. ARBRE includes a comprehensive biochemical reaction network centered around aromatic amino acid biosynthesis and a computational toolbox for pathway search, enzyme annotation, pathway ranking, visualization, and network expansion.
METABOLIC ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Mohammed N. Islam, Tianqu Zhai, Alexander Dobre, Cynthia N. Meah, Ioulia Kovelman, Steven Broglio, Daniel A. Beard, Xiaosu Hu, Jacob R. Joseph, Yamaan S. Saadeh, Rachel Russo, Hasan B. Alam
Summary: We propose a novel, noninvasive super-continuum infrared spectroscopy system that can simultaneously measure hemodynamic and metabolic parameters. Through laboratory tests, human studies, and animal studies, we demonstrate the utility of this system. It can measure the redox state of cytochrome c oxidase, as well as traditional markers such as oxygenated and deoxygenated hemoglobin.
APPLIED SCIENCES-BASEL
(2022)
Article
Multidisciplinary Sciences
Evangelia Vayena, Anush Chiappino-Pepe, Homa MohammadiPeyhani, Yannick Francioli, Noushin Hadadi, Meric Ataman, Jasmin Hafner, Stavros Pavlou, Vassily Hatzimanikatis
Summary: This study introduces a workflow called NICEgame for identifying and curating nonannotated metabolic functions in genomes. By providing alternative reaction sets and candidate genes, NICEgame can resolve gaps in metabolic models and improve genome annotation accuracy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S. H. Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R. Zecchini, Sabrina H. Rossi, Charlie Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent Gnanapragasam, Anne Y. Warren, Grant D. Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Summary: Metabolic flexibility occurs during ccRCC progression, and the reprogramming of branched-chain amino acid catabolism and urea cycle allows for metabolic flexibility in renal cancer progression.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Hyo Sub Choi, Ajay Bhat, Marshall B. Howington, Megan L. Schaller, Rebecca L. Cox, Shijiao Huang, Safa Beydoun, Hillary A. Miller, Angela M. Tuckowski, Joy Mecano, Elizabeth S. Dean, Lindy Jensen, Daniel A. Beard, Charles R. Evans, Scott F. Leiser
Summary: This study reveals that FMO-2 modifies endogenous metabolism through changes in one carbon metabolism, leading to increased lifespan and healthspan in C. elegans. Decreased methylation is identified as the major flux modified by FMO-2, which is sufficient to recapitulate its longevity benefits. It is also found that tryptophan, a validated substrate for FMO-2, is decreased in multiple mammalian FMO overexpression models. The study highlights the importance of FMOs in promoting health and longevity through metabolic remodeling.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Christopher J. Halbrook, Galloway Thurston, Seth Boyer, Cecily Anaraki, Jennifer A. Jimenez, Amy McCarthy, Nina G. Steele, Samuel A. Kerk, Hanna S. Hong, Lin Lin, Fiona V. Law, Catherine Felton, Lorenzo Scipioni, Peter Sajjakulnukit, Anthony Andren, Alica K. Beutel, Rima Singh, Barbara S. Nelson, Fran van den Bergh, Abigail S. Krall, Peter J. Mullen, Li Zhang, Sandeep Batra, Jennifer P. Morton, Ben Z. Stanger, Heather R. Christofk, Michelle A. Digman, Daniel A. Beard, Andrea Viale, Ji Zhang, Howard C. Crawford, Marina Pasca di Magliano, Claus Jorgensen, Costas A. Lyssiotis
Summary: Halbrook et al. identified two metabolic subgroups of pancreatic ductal adenocarcinoma cells based on differential integrated stress response and asparagine production, which enable symbiosis and resistance to phenformin. The study reveals the importance of metabolic adaptations in pancreatic cancer cells and provides insights into the potential for metabolic cross-talk among subgroups within the same tumor.
Article
Multidisciplinary Sciences
Asli Sahin, Daniel R. Weilandt, Vassily Hatzimanikatis
Summary: The authors introduce a framework to explore the optimal operating conditions of complex enzyme mechanisms from an evolutionary perspective. They use a mixed-integer formulation to assess the distribution of thermodynamic forces and enzyme states, providing detailed insights into enzymatic mode of operation. The framework can investigate the optimal catalytic properties of complex enzyme mechanisms.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Martin Schafer, Alan R. Pacheco, Rahel Kunzler, Miriam Bortfeld-Miller, Christopher M. Field, Evangelia Vayena, Vassily Hatzimanikatis, Julia A. Vorholt
Summary: Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria. The models recapitulated outcomes observed in planta with >89% accuracy, highlighting the role of carbon utilization and the contributions of niche partitioning and cross-feeding in the assembly of leaf microbiomes.
Meeting Abstract
Biophysics
Nicole L. Collins, Francoise Van den Bergh, Daniel A. Beard
BIOPHYSICAL JOURNAL
(2023)
Article
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.
Article
Computer Science, Artificial Intelligence
Subham Choudhury, Michael Moret, Pierre Salvy, Daniel Weilandt, Vassily Hatzimanikatis, Ljubisa Miskovic
Summary: Kinetic models of metabolism play a crucial role in understanding cellular physiology, but traditional kinetic modeling methods are unreliable and computationally inefficient due to lack of experimental data. A deep learning framework called REKINDLE efficiently generates dynamic kinetic models that match observed cellular behavior, providing new opportunities for studying cellular metabolic behavior.
NATURE MACHINE INTELLIGENCE
(2022)
