Graph transformation method for calculating waiting times in Markov chains

We describe an exact approach for calculating transition probabilities and waiting times in finite-state discrete-time Markov processes. All the states and the rules for transitions between them must be known in advance. We can then calculate averages over a given ensemble of paths for both additive and multiplicative properties in a nonstochastic and noniterative fashion. In particular, we can calculate the mean first-passage time between arbitrary groups of stationary points for discrete path sampling databases, and hence extract phenomenological rate constants. We present a number of examples to demonstrate the efficiency and robustness of this approach.     

Symmetrization of the AMBER and CHARMM force fields

The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly facilitate the bookkeeping associated with constructing kinetic transition networks via geometry optimization. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Analysis of cooperativity and localization for atomic rearrangements

We propose measures of localization and cooperativity for the analysis of atomic rearrangements. We show that for both clusters and bulk material cooperative rearrangements usually have significantly lower barriers than uncooperative ones, irrespective of the degree of localization. We also find that previous methods used to sample stationary points are biased towards rearrangements of particular types. Linear interpolation between local minima in double-ended transition state searches tends to produce cooperative rearrangements, while random perturbations of all the coordinates, as sometimes used in single-ended searches, have the opposite effect.     

Temperature-pressure phase diagram of a D2O-D2 system at pressures to 1.8 kbar

Using a volumetric technique, the deuterium solubility, X, in heavy water (L), low-pressure hexagonal ice (I h), and high-pressure cubic clathrate ice (sII) is studied at deuterium pressures up to 1.8 kbar and temperatures from -40 to +5 degrees C. The triple point of the L + I(h) + sII equilibrium is located at P = 1.07(3) kbar and T = -4.5(8) degrees C. The molar ratios D2/D2O of phases at the triple point are X(L) = 0.020(5), X(Ih) = 0.012(5), and X(sII) = 0.207(5).     

ProtSqueeze: simple and effective automated tool for setting up membrane protein simulations

The major challenge in setting up membrane protein simulations is embedding the protein into the pre-equilibrated lipid bilayer. Several techniques were proposed to achieve optimal packing of the lipid molecules around the protein. However, all of them possess serious disadvantages, which limit their applicability and discourage the users of simulation packages from using them. In the present work, we analyzed existing approaches and proposed a new procedure of protein insertion into the lipid bilayer, which is implemented in the ProtSqueeze software. The advantages of ProtSqueeze are as follows: (1) the insertion algorithm is simple, understandable, and controllable; (2) the software can work with virtually any simulation package on virtually any platform; (3) no modification of the source code of the simulation package is needed; (4) the procedure of insertion is as automated as possible; (5) ProtSqueeze is distributed for free under a general public license. In this work, we present the architecture and the algorithm of ProtSqueeze and demonstrate its usage in case studies.     

High resolution Fourier transform spectroscopy of HD16O: Line positions,absolute intensities and self broadening coefficients in the 8800–11,600 cm−1 spectral region

High-resolution water vapor absorption spectra have been measured at room temperature in the 8800–11,600 cm^?1 spectral region. They were obtained using the mobile BRUKER IFS 120M Fourier transform spectrometer (FTS) from ULB-SCQP coupled to the 50 m base long multiple reflection White type cell in GSMA laboratory. The absorption path was 600 m and different H₂O/HDO/D₂O mixtures were used. Measurements of line positions, intensities and self-broadening coefficients were performed for the HD¹⁶O isotopologue. 6464 rovibrational assignment of the observed lines was made on the basis of global variational predictions and allowed the identification of new energy levels. 3ν₃, 2ν₁+ν₃, 3ν₁+ν₂, ν₁+2ν₃ and 2ν₂+2ν₃ are the five strongest bands. The present paper provides a complementary data set on water vapor for atmospheric and astrophysical applications.     

Synthesis of hydrated furans: Analysis of the Prins reaction mechanism

Mechanistic analysis of hydrogenated furan synthesis by the Prins reaction was carried out using mathematical modeling. The direct and inverse chemical kinetic problems are solved for the rate constants of all elementary steps. A probable mechanism is derived from the obtained quantitative kinetic parameters and the kinetic patterns of the reaction. These include kinetic curves from the concentration changes of all species in the reaction.