Biothermodynamics and Mathematical modeling materials

Index

	Educational materials
	Reference books
	Research materials
	Conferences materials
	Personal pages
	Software

Educational materials

	The Metabolic Control Analysis Web These web pages contain a brief electronic review of metabolic control analysis (MCA) by P. Mendes.
	Guide to metabolic control analysis. Fundamentals of Enzyme Kinetics These pages are based closely on Chapter 10 of Fundamentals of Enzyme Kinetics (Athel Cornish-Bowden, 1995, Portland Press, London).
	Metabolic control analysis FAQ This page is intended as an elementary introduction to metabolic control analysis for people who have heard of metabolic control analysis but have very little idea of what it is.

	Introduction to Macromolecular Simulation The purpose of this tutorial is to introduce several popular numerical techniques used to simulate the structure and dynamics of biomolecules. The discussion is confined to simulation methods that apply classical mechanics to biological systems, although some quantum theory is presented to quantify some shortcomings of classical approximations. Molecular dynamics (MD) simulation, Langevin dynamics (LD) simulation, Monte Carlo (MC) simulation, and normal mode analysis are among the methods surveyed here.
	METABOLOMICS IN ABERYSTWYTH Whilst there is much current interest in the genome-wide analysis of cells at the level of transcription (to define the 'transcriptome') and translation (to define the 'proteome'), the third level of analysis, that of the 'metabolome', has been curiously unexplored to date. The term 'metabolome' refers to the entire complement of all the small molecular weight metabolites inside a cell suspension (or other sample) of interest. It is likely that measurement of the metabolome in different physiological states will in fact be much more discriminating for the purposes of functional genomics.
	Computers for Biochemists & Molecular Biologists. Course of lectures This course is being developed by B. Tracy Nixon (btn1@psu.edu). Two prior versions were offered in the Fall of 1995, 1996 and 1997. It is being offered again in the Fall of 1998 in two sections.
	Simulation of metabolic systems (by Pedro Mendes) Work in the following areas: 1. Construction of a biochemical kinetics simulation program (GEPASI). 2. Usage of simulation to study protein-protein interactions, more specifically metabolite channelling 3. simulation of heterogeneous spatio-temporal biochemical models. Another area actively involved is Metabolic Control Analysis. MCA can be used both to analyze experimental results and to characterize results from simulations.
	GEPASI (developed by Pedro Mendes) a user- friendly MS- Windows computer program to simulate the dynamics of biochemical systems, with an emphasis on the steady- state properties of pathways containing enzymes that interact by transferring their intermediate metabolite directly (metabolic channelling).

Recommendations for nomenclature and tables in biochemical thermodynamics (1994)
IUBMB-IUPAC JOINT COMMISSION ON BIOCHEMICAL NOMENCLATURE (JCBN). The recommendations in this version are identical to those in the published document prepared by Robert A. Alberty (Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA), see Eur. J. Biochem., 1996, 240, 1-14; 242, 433; Pure Appl. Chem. 1994, 66, 1641-1666 [Copyright IUBMB and IUPAC].

Research materials

	Biochemistry (Moscow) On-Line, World Wide Web version of the international edition of Russian leading scientific journal in the fields of biochemistry and biochemical aspects of molecular biology, bioorganic chemistry, microbiology, immunology, physiology, and biomedical sciences. Some articles available in full text (in HTML)
	Theoretical Biophysics group Light Harvesting in Bacterial Photosynthesis
	George Oster. University of California Department of Molecular and Cellular Biology Mathematical modeling of ATP synthase. Bibliography with full-text articles. Software description.
	Hongyun Wang's Home Page (Works with G. Oster) Mathematical modeling of ATP synthase. Bibliography with full-text articles. Links to ATPase work movies - more than 20!!! (in MPEG and AVI format).
	Metabolic Control Analysis Research Group (Headed by D. Fell) The group. News. Introduction. Projects. Publications (New items 18 Feb. 1999). Software. Group members. Links to other control analysis research.
	Pedro Mendes Homepage computer simulation of biochemical processes, protein-protein interactions especially metabolic channeling, enzymology, nonlinear dynamics, metabolic control analysis, gene expression.
	Simulation of metabolic systems (by Pedro Mendes) Work in the following areas: 1. Construction of a biochemical kinetics simulation program (GEPASI). 2. Usage of simulation to study protein-protein interactions, more specifically metabolite channelling 3. simulation of heterogeneous spatio-temporal biochemical models. Another area actively involved is Metabolic Control Analysis. MCA can be used both to analyze experimental results and to characterize results from simulations.

Conferences materials

	Workshop on theoretical biophysics Hiddensee, April 1 - 4 1998 Programme and Abstracts
	Hiddensee Workshop of the Graduiertenkolleg "Dynamics and evolution of cellular and macromolecular processes" March, 17-19, 1999 Programme only
	3rd Berlin Workshop on Theoretical Biophysics (1996) Programme and abstracts. The main topics are: Nonlinear dynamics (calcium oscillations and waves, synchronization of cellular oscillations, minimal models of oscillations), evolutionary optimization of enzymatic systems, metabolic control analysis and kinetic modelling, flux modes in chemical reaction networks, Molecular dynamics of proteins, DNA sequences, membrane dynamics, Evolutionary game theory, modelling of signal transduction in the visual cascade.
	MCA 99 NATO Advanced Research Workshop on Technological and Medical Implications of Metabolic Control Analysis This page contains information about the NATO Advanced Research Workshop in April 1999 at Visegrad, Hungary. Programme, abstracts, poster texts, detailed information about participants.
	What is Controlling Life? 50 years after Erwin Schrödinger's What is Life? Modern Trends in BioThermoKinetics Volume 3 Series edited by the International BioThermoKinetics Study Group (1994). Scope: Modern Trends in BioThermoKinetics deals with developments in biological thermodynamics, kinetics, metabolic regulation and control. It is aimed at promoting the understanding and application of bioenergetics, including theory, models, computation, instrumentation, experiment and generalized concepts. Applications of bioenergetics are discussed in relation to physiology, medicine, ecology and biotechnology. Interdisciplinary integration and international cooperation visibly characterize the contributions published in this series which thus conveys the spirit of an ongoing process of scientific enterprise rather than the static picture of closed chapters in science.

Personal pages

JD Lab page
Our lab at UT Southwestern. We study the three-dimensional structures of biological macromolecules with the methods of X-ray crystallography. Among the techniques we use are heterologous expression, purification, crystallization, and mutagenesis of proteins, X-ray diffraction, computational crystallography, and structure analysis. Our interests focus on the following main areas: Proteins involved in energy transfer and electron transfer, proteins using light energy, membrane proteins, membrane associating proteins, chaperonins and proteins with repeating sequence motifs.

	George Oster. University of California Department of Molecular and Cellular Biology Mathematical modeling of ATP synthase. Bibliography with full-text articles. Software description.
	Hongyun Wang's Home Page (Works with G. Oster) Mathematical modeling of ATP synthase. Bibliography with full-text articles. Links to ATPase work movies - more than 20!!! (in MPEG and AVI format).
	Metabolic Control Analysis Research Group (Headed by D. Fell) The group. News. Introduction. Projects. Publications (New items 18 Feb. 1999). Software. Group members. Links to other control analysis research.
	Pedro Mendes Homepage computer simulation of biochemical processes, protein-protein interactions especially metabolic channeling, enzymology, nonlinear dynamics, metabolic control analysis, gene expression.
	Prof. Reinhart Heinrich Homepage The Regulation of Cellular Systems, Mathematical modeling

Software

	METATOOL - HOMEPAGE Metatool is a program for studying structural properties of metabolic networks by using methods of linear and convex algebra. The theoretical background of the program and examples are given under publications and literature, for details of the algorithms and a description of the program follow the metatool description link.
	GEPASI - Powerful software system for the simulation of chemical and biochemical kinetics (written by Pedro Mendes)
	Berkeley Madonna program (ODE solver) - program for fast solving differential equations. Berkeley Madonna was conceived and developed by Robert Macey and George Oster of the University of California at Berkeley. Programmed by Tim Zahnley. See description on the page Berkeley Madonna program
	XSIM - Biochemistry modeling program. See description at the site of National Simulation Resource, University of Washington
	Calculator 98 - Calc98 is a pocket calculator simulator program for the Microsoft Windows operating system, with many additional features and greater flexibility. It is especially designed for scientific and engineering users and includes a wide range of units conversions and scientific functions. It also has statistics, financial and time functions.
	Molecular weights calculator by Matthew Monroe - necessary tool for lab - calculates substances weight, concentration, molarity