MIND0/3 Study of the \u27Thermal Rearrangements of Bicyclobutanylidene

It is found that path (i), which is concerted and stereospecific, is favored both thermodynamically and kinetically, in agreement with exp~\u27rimental results. In addition, paths (ii) and (iii) are found to be competitive with each other and both are highly energetic due to steric effects, with activation energy being about 50 kcal/mo!

MIND0/3 Study of the \u27Thermal Rearrangements of Bicyclobutanylidene

It is found that path (i), which is concerted and stereospecific, is favored both thermodynamically and kinetically, in agreement with exp~\u27rimental results. In addition, paths (ii) and (iii) are found to be competitive with each other and both are highly energetic due to steric effects, with activation energy being about 50 kcal/mo!

Simulation Study of a Gramicidin/Lipid Bilayer System in Excess Water and Lipid. II. Rates and Mechanisms of Water Transport

AbstractA gramicidin channel in a fluid phase DMPC bilayer with excess lipid and water has been simulated. By use of the formal correspondence between diffusion and random walk, a permeability for water through the channel was calculated, and was found to agree closely with the experimental results of Rosenberg and Finkelstein (Rosenberg, P. A., and A. Finkelstein. 1978. J. Gen. Physiol. 72:327–340; 341–350) for permeation of water through gramicidin in a phospholipid membrane. By using fluctuation analysis, components of resistance to permeation were computed for movement through the channel interior, for the transition step at the channel mouth where the water molecule solvation environment changes, and for the process of diffusion up to the channel mouth. The majority of the resistance to permeation appears to occur in the transition step at the channel mouth. A significant amount is also due to structurally based free energy barriers within the channel. Only small amounts are due to local friction within the channel or to diffusive resistance for approaching the channel mouth

MNDO Study of Helvetane and Israelane

Applying MNDO approximatlon, the heats of formation (LlHt) and structures of the navel compounds helvetane (1) and israelane (2) have been calculated. The MNDO sn, for 1 and 2 are 336 and 719 kcal/mol, respectively, in agreement with the previous prediction that 1 is more stable than 2. In addition, in view of the structures calculated, the large positive LlHt values of 1 and 2 are most likely the result of these malecules\u27 angular strain

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method

<p>Abstract</p> <p>Background</p> <p>Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction.</p> <p>Results</p> <p>We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of ~20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring function yielding best selection accuracy in the decoy sets, the POC method yields 23%, 37%, and 64% less false positives in distinguishing the native conformation, indentifying a near-native model (RMSD < 0.5A from the native) as top-ranked, and selecting at least one near-native model in the top-5-ranked models, respectively. Similar effectiveness of the POC method is also found in the decoy sets from membrane protein loops. Furthermore, the POC method outperforms the other popularly-used consensus strategies in model ranking, such as rank-by-number, rank-by-rank, rank-by-vote, and regression-based methods.</p> <p>Conclusions</p> <p>By integrating multiple knowledge- and physics-based scoring functions based on Pareto optimality and fuzzy dominance, the POC method is effective in distinguishing the best loop models from the other ones within a loop model set.</p

What Drives Animal Fluency Performance in Cantonese-Speaking Chinese Patients with Adult-Onset Psychosis?

Among the numerous studies investigating semantic factors associated with functioning in psychotic patients, most have been conducted on western populations. By contrast, the current cross-sectional study involved native Cantonese-speaking Chinese participants. Using the category fluency task, we compared performance between patients and healthy participants and examined clinical and sociodemographic correlates. First-episode psychosis patients (n = 356) and gender- and age-matched healthy participants (n = 35) were asked to generate as many ‘animals’ as they could in a minute. As expected, patients generated fewer correct responses (an average of 15.5 vs. 22.9 words), generated fewer clusters (an average of 3.7 vs. 5.4 thematically grouped nouns), switched less between clusters (on average 8.0 vs. 11.9 switches) and, interestingly, produced a larger percentage of Chinese zodiac animals than healthy participants (an average of 37.7 vs. 24.2). However, these significant group differences in the clusters and switches disappeared when the overall word production was controlled for. Within patients, education was the strongest predictor of category fluency performance (namely the number of correct responses, clusters, and switches). The findings suggest that an overall slowness in patients may account for the group differences in category fluency performance rather than any specific abnormality per se

MODEL ELECTRON-POSITRON CORRELATION POTENTIAL FOR LOW-ENERGY POSITRON-ATOM ELASTIC SCATTERING

The wave function for positron-atom scattering is approximated in the trial form of (UNFORMATTED TABLE FOLLOWS) (PSI)((\u27)r(,e),(\u27)r(,p)) = (psi)((\u27)r(,e),(\u27)r(,p))(psi)(r(,p)). (1)(TABLE ENDS) The closed-channel function (psi)((\u27)r(,e),(\u27)r(,p)), a determinant of electronic function (phi)(,i), and the open-channel function (psi)((\u27)r(,p)) can be found by applying the Hartree-Fock (HF) variational principle, (delta) (INT) (PSI)H(PSI)d(tau) = 0, subject to orthonormality constraints on the (phi)(,i)\u27s leads to uncoupled Schrodinger equations for the electrons and the positron. The positronic operators are replaced by a model potential V(,mp) in the Schrodinger equation for the electronic part, (DIAGRAM, TABLE OR GRAPHIC OMITTED...PLEASE SEE DAI) where the Coulomb ((\u27)J(,j)) and exchange ((\u27)K(,j)) integrals are r(,p)-dependent. The proposed functional form of V(,mp) is (UNFORMATTED TABLE FOLLOWS) V(,mp)(r(,p),r(,(mu)p)) = 1 - ce(,n)(\u27x)e(\u27-x) (be(\u27-ar(,(mu)p))/r(,(mu)p)), x = r(,p)/r(,0), (3)(TABLE ENDS) where a, b, c, r(,0), and n are disposable parameters and (DIAGRAM, TABLE OR GRAPHIC OMITTED...PLEASE SEE DAI) The Schrodinger equation for the positron is a potential scattering equation: (UNFORMATTED TABLE FOLLOWS) -1/2(DEL)(,p)(\u272) + Z/r(,p) + V(,ep)(r(,p)) - k(\u272)/2 (phi)(,p)((\u27)k,(\u27)r(,p)). (4)(TABLE ENDS) The effective electron-positron interaction potential V(,ep) is obtained by subtracting the HF ground-state energy from the r(,p)-dependent electronic energy obtained by solving eq. (2). The parameters for V(,mp) are found such that the calculated V(,ep) leads to the known scattering lengths for the H-e(\u27+) and He-e(\u27+) systems. The calculated results for cross sections and annihilation parameters for both test systems are reasonably good as compared to other variational and approximate methods. The present results also suggest the model framework can be extended to other larger positron-atom systems