Divesh Bhatt

Monte Carlo simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB): Pressure and temperature effects for the solid phase and vapor-liquid phase equilibria

The transferable potentials for phase equilibria (TraPPE) force field was extended to nitro and amino substituents for aromatic rings via parametrization to the vapor-liquid coexistence curves of nitrobenzene and aniline, respectively. These groups were then transferred to model 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Without any further parametrization to solid state data, the TraPPE force field is able to predict TATBs unit cell lengths and angles at 295 K with mean unsigned percentage errors of 0.3% and 1.8% and the specific density within 0.5%. These predictions are comparable in accuracy to the GRBF model [Gee et al., J. Chem. Phys. 120, 7059 (2004)] that was parametrized directly to TATBs solid state properties. Both force fields are able to reproduce the pressure dependence of TATBs unit cell volume, but they underestimate its thermal expansion. Due to its energetic nature and unusually large cohesive energy, TATB is not chemically stable at temperature in its liquid range. Gibbs ensemble simulations allow one to determine TATBs vapor-liquid coexistence curve at elevated temperatures and the predicted critical temperature and density for the TraPPE and GRBF model are 937+/-8 and 1034+/-8 K, and 0.52+/-0.02 and 0.50+/-0.02 gcm(3), respectively.

Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies

Developing pharmacological strategies for controlling ionizing radiation (IR)-induced cell death is important for both mitigating radiation damage and alleviating the side effects of anti-cancer radiotherapy manifested in surrounding tissue morbidity. Exposure to IR often triggers the onset of p53-dependent apoptotic pathways. Here we build a stochastic model of p53 induced apoptosis comprised of coupled modules of nuclear p53 activation, mitochondrial cytochrome c release and cytosolic caspase activation that also takes into account cellular heterogeneity. Our simulations show that the strength of p53 transcriptional activity and its coupling (or timing with respect) to mitochondrial pore opening are major determinants of cell fate: for systems where apoptosis is elicited via a p53-transcription-independent mechanism, direct activation of Bax by p53 becomes critical to IR-induced-damage initiation. We further show that immediate administration of PUMA inhibitors following IR exposure effectively suppresses excessive cell death, provided that there is a strong caspase/Bid feedback loop; however, the efficacy of the treatment diminishes with increasing delay in treatment implementation. In contrast, the combined inhibition of Bid and Bax elicits an anti-apoptotic response that is effective over a range of time delays.

An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.

We introduce an adaptive weighted-ensemble procedure (aWEP) for efficient and accurate evaluation of first-passage rates between states for two-state systems. The basic idea that distinguishes aWEP from conventional weighted-ensemble (WE) methodology is the division of the configuration space into smaller regions and equilibration of the trajectories within each region upon adaptive partitioning of the regions themselves into small grids. The equilibrated conditional∕transition probabilities between each pair of regions lead to the determination of populations of the regions and the first-passage times between regions, which in turn are combined to evaluate the first passage times for the forward and backward transitions between the two states. The application of the procedure to a non-trivial coarse-grained model of a 70-residue calcium binding domain of calmodulin is shown to efficiently yield information on the equilibrium probabilities of the two states as well as their first passage times. Notably, the new procedure is significantly more efficient than the canonical implementation of the WE procedure, and this improvement becomes even more significant at low temperatures.