Why Fire Is Hot

A recent paper by K. Schmidt-Rohr (Chemistry) answered the question why combustion reactions are always exothermic.  Every scientist should be able to explain what makes fire hot, but neither chemistry nor combustion textbooks have provided a valid answer. Schmidt-Rohr’s analysis shows that the reason lies in the double bond in O2, which is much weaker than other double bonds or pairs of single bonds in the biosphere, so that the formation of the stronger bonds in CO2 and H2O results in the release of heat. The bond energies in the fuel play only a minor role; e.g., the total bond energy of CH4 is nearly the same as that of CO2. A systematic analysis of bond energies gives the heat of combustion close to –418 kJ (i.e., –100 kcal) per mol O2, in good agreement (±3%) with data for >500 organic compounds; the heat of condensation of H2O (–44 kJ per mol H2O(l)) is also included in the analysis. For 268 molecules with ≥8 carbon atoms, the standard deviation is even smaller, 2.1%. For a fuel of composition CcHhOoNn, this gives DcH ≈ -418 kJ (c + 0.3 h – 0.5 o), which enables instant estimates of heats of combustion simply from the elemental composition, even for complex mixtures of unknown molecular composition, and explains principles of biofuels production. The analysis indicates that O2, rather than fuels like octane, H2, ethanol, or glucose, is the crucial “energy-rich” molecule. It also challenges common notions about a relation between the oxidation state and the energy content of biomolecules.


One then needs to explain why O2 is abundant in air despite its high enthalpy: All the O2 in the earth’s atmosphere has been produced by photosynthesis in cyanobacteria, algae, and higher plants, as a by-product of photosynthetic proton and electron production from H2O. The “price” of the production of O2, which is energetically so unfavorable, is paid by plants and algae (with “cheap” energy from the sun) in order to be able to live wherever H2O is present. So one can conclude that atmospheric O2 stores solar energy that sustains us with every breath we take.

Schmidt-Rohr K. Why Combustions Are Always Exothermic, Yielding About 418 kJ per Mole of O-2. J Chem Educ. 2015;92(12):2094-9.

Why nanorods assemble

In a recent paper in Phys. Rev. E, Brandeis postdoc Yasheng Yang and Assistant Professor of Physics Michael Hagan developed a theory to describe the assembly behavior of colloidal rods (i.e. nanorods) in the presence of inert polymer (which induces attractions between the nanorods). The nanorods assemble into several kinds of structures, including colloidal membranes, which  are two dimensional membrane-like structures composed of a one rod-length thick monolayer of aligned rods.  The theory shows that colloidal membranes are stabilized against stacking on top of each other by an entropic force arising from protrusions of rods from the membranes and that there is a critical aspect ratio (rod length/rod diameter) below which membranes are never stable. Understanding the forces that stabilize colloidal membranes is of practical importance since these structures could enable the manufacture of inexpensive and easily scalable optoelectronic devices. This work was part of a collaboration with the experimental lab of Zvonimir Dogic at Brandeis, where colloidal membranes are developed and studied.

Yang YS, Hagan MF. Theoretical calculation of the phase behavior of colloidal membranes. Phys Rev E. 2011;84(5).

Dynamics of double-strand break repair

In a new paper in the journal Genetics, former Brandeis postdoc Eric Coïc and undergrads Taehyun Ryu and Sue Yen Tay from Professor of Biology Jim Haber’s lab, along with grad student Joshua Martin and Professor of Physics Jané Kondev, tackle the problem of understanding the dynamics of homologous recombination after double strand breaks in yeast. According to Haber,

The accurate repair of chromosome breaks is an essential process that prevents cells from undergoing gross chromosomal rearrangements that are the hallmark of most cancer cells.  We know a lot about how such breaks are repaired.  The ends of the break are resected and provide a platform for the assembly of many copies of the key recombination protein, Rad51.  Somehow the Rad51 filament is then able to facilitate a search of the entire DNA of the nucleus to locate identical or nearly identical (homologous) sequences so that the broken end can pair up with this template and initiate local copying of this segment to patch up the chromosome break.  How this search takes place remains poorly understood.

The switching of budding yeast mating type genes has been a valuable model system in which to study the molecular events of broken chromosome repair, in real time.  It is possible to induce synchronously a site-specific double-strand break (DSB) on one chromosome, within the mating-type (MAT) locus.  At opposite ends of the same chromosome are two competing donor sequences with which the broken ends of the MAT sequence can pair up and copy new mating-type sequences into the MAT locus.

Normally one of these donors is used 9 times more often than the other.  We asked if this preference was irrevocable or if the bias could be changed by making the “wrong” donor more attractive – in this case by adding more sequences to that donor so that it shared more and more homology with the broken ends at MAT.  We found that the competition could indeed be changed and that adding more homologous sequences to the poorly-used donor increased its use.

In collaboration with Jané Kondev’s lab we devised both a “toy” model and a more rigorous thermodynamic model to explain these results.  They suggest that the Rad51 filament carrying the broken end of the MAT locus collides on average 4 times before with the preferred donor region before it actually succeeds in carrying out the next steps in the process that lead to repair and MAT switching.

Dynamics of homology searching during gene conversion in Saccharomyces cerevisiae revealed by donor competition Eric Coïc , Joshua Martin, Taehyun Ryu, Sue Yen Tay, Jané Kondev and James E. Haber. Genetics. 2011 Sep 27 2011 Sep 27

New courses, Fall 2011

New courses offered in the Division of Science in Fall, 2011:

BISC 9B Biology of Cancer (Dore)

Introduces the fundamental aspects of cancer development, progression and treatment with an emphasis on the cellular and molecular changes thought to lead to cancer. Both genetic and lifestyle factors and their impact on the predisposition to develop and recover from cancer will be discussed. Usually offered every year.

CBIO 101A  Chemical Biology (Pontrello)

Chemical biology is not just biochemistry, and the subject involves much more than a simple combination of chemistry and biology topics. This course will explore how recent cutting edge scientific work in chemistry has led to a deeper fundamental understanding of and ability to manipulate biological processes. Emphasis will be placed on the design and chemical synthesis of micro and macromolecular structures that allow scientists to ask unique chemical and biological questions as well as to control biological systems. Both synthetic strategies and characterization as well as biological evaluation and utility will be discussed. The course will consist of scientific literature readings, periodic assignments and exams based on literature and lecture content, as well as group projects and exercises. A textbook is not required, although retention of prerequisite course textbooks is strongly recommended. Topics will range from fluorescent probes, chemical inducers of dimerization, bacterial chemotaxis, controlling stem cell differentiation, solid phase synthesis, synthetic nucleotides, B cell activation, and chemical-inducers of dimerization, just to name a few.

This is not an introductory science course, and the structure will be designed to enhance student understanding of the subject through primary literature and group discussion and review. After several instructor lectures covering general chemistry and biology background, each class will be structured around student presentations of assigned primary scientific literature as a starting point for class discussion about the area of research. The course will also include a project where each student will search chemical biology journals, select a recent article they find interesting, and prepare a report explaining background, fundamental chemistry and biology addressed in the paper, results and applications, and also future directions and implications for the field. The final exam will be based on the content of this collective work.

BCHM 104A Physical Chemistry of Macromolecules I (C.Miller, Oprian)

Covers basics of physical chemistry underpinning applications in BCHM 104b. Focus is placed on quantitative treatments of the probabilistic nature of molecular reality: molecular kinetic theory, basic statistical mechanics, and chemical thermodynamics in aqueous solution. Usually offered every second year

BIOL 107A Data Analysis and Statistics Workshop (Van Hooser)

The interpretation of data is key to making new discoveries, making optimal decisions, and designing experiments. Students will learn skills of data analysis through hands-on, computer-based tutorials and exercises that include experimental data from the biological sciences. Knowledge of very basic statistics (mean, median) will be assumed. Usually offered every second year.

BCHM 172A Cholesterol in Health and Disease (Westover)

In today’s supermarkets, many foods are proudly labeled “cholesterol-free.” 1in 4 Americans over 45 take medicine to lower their cholesterol levels.  Yet, every beginning biology student learns that cholesterol is an essential component of mammalian cell membranes.

This fall, the Biochemistry Department’s Emily Westover will teach a new course called Cholesterol in Health and Disease, BCHM 172a. Drawing from the current literature, students in this course will explore many facets of cholesterol science.  This course will be case study in cholesterol, bringing together concepts from a variety of disciplines, including cell biology, biophysics, biochemistry, physiology and medicine.

The class will address questions such as:

  • How does the body balance production and dietary uptake of cholesterol?
  • What effects does cholesterol have on membrane and protein function?
  • What is the connection between cholesterol and atherosclerosis?

BCHM 172 will meet Tuesdays at 2 pm in the 4th floor Ros-Kos Conference Room.

NBIO 157A Project Laboratory in Neurobiology and Behavior (Vecsey)

What is it like to be a scientist?

Many college science courses don’t help students answer that question. In lecture courses, a host of scientific facts are taught via textbook, but at the end of the course students have read little if any primary research, and would be hard-pressed to explain in detail how those facts were discovered. Courses with labs often have “recipe books” that lay out all of the necessary ingredients and steps required to achieve a desired experimental result. Even students who try to get scientific training by working in a lab may at first be relegated to perform menial tasks that are not fully representative of the scientific process.

With all of this in mind, Brandeis University introduced a series of courses called Project Labs. In these courses, students carry out legitimate research projects in a range of disciplines. No cookbooks, no expected outcomes. We start with an introduction to a biological question, and then set about answering it. We read primary literature to understand the basis for the research we will carry out, and we write up the results in a true journal format.

The newest installment in the Project Lab series is Bio157a, the Project Lab in Neurobiology and Behavior. In this course, the ultimate goal is to understand how an animal like the fruit fly senses and responds to temperature. Specifically, we will examine temperature preference behavior in Drosophila melanogaster and several related species. Some of those species are native to cold climates, whereas others hail from deserts such as the Mojave. Have these species evolved to prefer different temperatures? Or are they simply more tolerant of those temperatures? These are some of the core questions that we will address. What the results will be we can only guess – and that’s what it’s like to be a scientist!

Protected by Akismet
Blog with WordPress

Welcome Guest | Login (Brandeis Members Only)