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Circular dichroism (CD) is the differential absorption of left and right circularly polarized light. It arises from molecular electron oscillations that are driven by both the light's electric and magnetic fields, where the effects are in phase for one circular polarization and out of phase for the other. We describe these interactions, which have not been presented at an intuitive level before, with classical and quantum treatments. A rotational average of the latter solution leads to the Rosenfeld equation, which underlies most CD research. We illustrate its use with a chiral version of a harmonic oscillator, which we then apply to the far-ultraviolet CD of protein [alpha]-helices. This presentation is aimed at the level of upper-division undergraduates and could be usefully incorporated into a physical chemistry course.

Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells.

The mathematics behind the average absorption cross-section is exactly one third of the maximum value described. The goal is to calculate experimental observables, or other properties of bulk sample, in terms of microscopic molecular parameters.

We describe the use of a computational model to study the effects of cellular architecture and macromolecular crowding on signal transduction in Escherichia coli chemotaxis. A newly developed program, Smoldyn, allows the movement and interaction of a large number of individual molecules in a structured environment to be simulated (S. S. Andrews and D. Bray, Phys. Biol., in press). With Smoldyn, we constructed a three-dimensional model of an E. coli cell and examined the diffusion of CheYp from the cluster of receptors to the flagellar motors under control conditions and in response to attractant and repellent stimuli. Our simulations agree well with experimental observations of cell swimming responses and are consistent with the diffusive behavior expected in wild-type and mutant cells. The high resolution available to us in the new program allows us to calculate the loci of individual CheYp molecules in a cell and the distribution of their lifetimes under different cellular conditions. We find that the time delay between stimulus and response differs for flagellar motors located at different positions in the ceil. We explore different possible locations for the phosphatase CheZ and show conditions under which a gradient of CheYp exists in the cell. The introduction of inert blocks into the cytoplasm, representing impenetrable structures such as the nucleoid and large protein complexes, produces a fall in the apparent diffusion coefficient of CheYp and enhances the differences between motors. These and other results are left as predictions for future experiments.

The initial electron transfer reaction in bacterial photosynthesis follows the electronic excitation of a strongly interacting pair of bacteriochlorophylls known as the special pair, or P. The stark spectrum of the intervalence band of the special pair radical cation in bacterial photosynthetic reaction centers is presented.

Issues concerning changes in vibrational frequency which can be interpreted by measuring the vibrational Stark effect in proteins are discussed.

Motivation Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ application programming interface (API), which were convenient, but limited extensibility. Results We added a Python API to Smoldyn to improve integration with other software tools, such as Jupyter notebooks, other Python code libraries and other simulators. It includes low-level functions that closely mimic the existing C/C++ API and higher-level functions that are more convenient to use. These latter functions follow modern object-oriented Python conventions. Availability and implementation Smoldyn is open source and free, available at http://www.smoldyn.org and can be installed with the Python package manager pip. It runs on Mac, Windows and Linux.   Documentation is available at http://www.smoldyn.org/SmoldynManual.pdf and https://smoldyn.readthedocs.io/en/latest/python/api.html. [ABSTRACT FROM AUTHOR]