Concept

Equilibrium thermodynamics

Related publications (43)

Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Noushin Hadadi, Milenko Tokic

In an effort of overcoming the limited availability of fossil energy resources the focus of the research and development in the area of biofuels has moved towards developing the second generation of fuels that should be produced via microbial fermentation. ...

2016

Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology

Meriç Ataman

Metabolism is a network of biochemical reactions that converts carbon sources to cellu-lar fuels and building blocks. Metabolism of many organisms has been studied for many decades. These studies define metabolism as a very large and complex network. Stoic ...

EPFL2016

Non-equilibrium conformational dynamics in the function of molecular chaperones

Paolo De Los Rios, Alessandro Barducci

Why do chaperones need ATP hydrolysis to help proteins reach their native, functional states? In this review, we highlight the most recent experimental and theoretical evidences suggesting that ATP hydrolysis allows molecular chaperones to escape the bound ...

Elsevier2015

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

Vassily Hatzimanikatis, Meriç Ataman

Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network ...

Elsevier2015

Study on how underlying uncertainty in the flux values affects metabolic control analysis of optimally grown E. coli

Ljubisa Miskovic, Meriç Ataman, Georgios Fengos, Tuure Eelis Hameri

Large-scale kinetic models of metabolism are essential for understanding and predicting the behavior of cellular systems when subject to perturbations. Despite the advances in experimental measurement technologies, the numerous parameters that are required ...

2015

Predicting aqueous speciation of environmentally relevant halogen oxidants: chloramines, bromamines, and bromochloramines

Jeremy Samuel Arey, Daniela Trogolo

Chloramines, bromamines, and bromochloramines are halogen-containing oxidants that arise from the reaction between ammonia and hypohalous acids during the disinfection of drinking and wastewaters. Although involved in the formation of toxic disinfection by ...

2015

A Study of Dynamic Responses of E. coli Metabolism Upon Large Perturbations Using Large-Scale Kinetic Models

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Fengos, Milenko Tokic

In recent years, constraint-based approaches have been widely used for analyzing cellular metabolism. These approaches use stoichiometric models for the characterization of the intracellular fluxes at steady state. Nonetheless, the stoichiometric models la ...

2015

The design of “Super E. coli” through automated reaction network generation and genome scale models

Vassily Hatzimanikatis, Noushin Hadadi, Keng Cher Soh

Genome-scale metabolic reconstructions capture the known metabolic capabilities of organisms and their analysis have provided many insights into complex biochemical networks. However, this approach relies on a database of known biochemical reactions and he ...

2014

In silico analysis of the interplay between P/O ratio and physiological states of the optimally grown Escherichia coli

Ljubisa Miskovic, Meriç Ataman, Keng Cher Soh, Stefano Andreozzi

The bioenergetics efficiency of aerobic respiration of an organism is expressed through P/O ratio, which represents the ATP production per oxygen atom reduced in Electron Transport Chains (ETC). P/O ratio, to date, has not been extensively used in the cont ...

2013

Towards the Glass Transition in Vibrated Granular Matter

Alessandro Luigi Sellerio

Granular materials are large sets of macroscopic particles that interact solely via contact forces. The static behavior depends on the contact network and on the surface friction forces between grains; when they are set in motion (typically by vibrations) ...

EPFL2012

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