We implemented the well-known Ising model in one dimension as a computer program and simulated its behavior with four algorithms: (i) the seminal Metropolis algorithm; (ii) the microcanonical algorithm described by Creutz in 1983; (iii) a variation on Creutz’s time-reversible algorithm allowing for bonds between spins to change dynamically; and (iv) a combination of the latter two algorithms in a manner reflecting the different timescales on which these two processes occur (“freezing” the bonds in place for part of the simulation). All variations on Creutz’s algorithm were symmetrical in time, and thus reversible. The first three algorithms all favored low-energy states of the spin lattice and generated the Boltzmann energy distribution after reaching thermal equilibrium, as expected, while the last algorithm broke from the Boltzmann distribution while the bonds were “frozen.” The interpretation of this result as a net increase to the system’s total entropy is consistent with the second law of thermodynamics, which leads to the relationship between maximum entropy and the Boltzmann distribution.

The photodissociation of 1-bromobutane is explored using pump-probe spectroscopy and time-of-flight mass spectrometry. Fragments of bromobutane are constructed computationally and theoretical energies are calculated using Gaussian 16 software. It is determined that the dissociation of bromine from the parent molecule is the most observed fragmentation pathway arising from the excitation of the ground state parent molecule to a dissociative A state using two 400 nm, 3.1 eV pump photons. The dissociation energy of this pathway is 2.91 eV, leaving 3.3 eV of energy that is redistributed into the product fragments as vibrational energy. C4H9 has the highest relative intensity in the mass spectrum with a relative intensity of 1.00. It is followed by C2H5 and C2H4 at relative intensities of 0.73 and 0.29 respectively. Because of the negative correlation between C4H9 and these two fragments at positive time delays, it is concluded that most of these smaller molecules are formed from the further dissociation of the fragment C4H9 rather than any alternative pathways from the parent molecule. Thermodynamic analysis of these pathways has displayed the power of thermodynamic prediction as well as its limitations as it fails to consider kinetic limitations in dissociation reactions.

Plant-made virus-like particles (VLPs), composed of HIV-1 Gag and deconstructed gp41 proteins, have been shown to be safe and immunogenic in mice. Here, we report the successful production of HIV-1 Gag/dgp41 VLPs in Nicotiana benthamiana, using an enhanced geminivirus-based expression vector. This novel vector results in unique expression kinetics, with peak protein accumulation and minimal necrosis achieved on day 4 post-infiltration. In comparing various purification strategies, it was determined that a 20% ammonium sulfate precipitation is an effective and efficient method for removing plant proteins and purifying the recombinant VLPs of interest. If further purification is required, this may be achieved through ultracentrifugation. VLPs are a useful platform for a variety of biomedical applications and developing the technology to efficiently produce VLPs in the plant expression system is of critical importance.