A memory based random walk model to understand diffusion in crowded heterogeneous environment

We study memory based random walk models to understand diffusive motion in crowded heterogeneous environment. The models considered are non-Markovian as the current move of the random walk models is determined by randomly selecting a move from history. At each step, particle can take right, left or stay moves which is correlated with the randomly selected past step. There is a perfect stay-stay correlation which ensures that the particle does not move if the randomly selected past step is a stay move. The probability of traversing the same direction as the chosen history or reversing it depends on the current time and the time or position of the history selected. The time or position dependent biasing in moves implicitly corresponds to the heterogeneity of the environment and dictates the long-time behavior of the dynamics that can be diffusive, sub or super diffusive. A combination of analytical solution and Monte Carlo simulation of different random walk models gives rich insight on the effects of correlations on the dynamics of a system in heterogeneous environment

Densely ball remotal subspaces of C(K)

AbstractWe call a subspace Y of a Banach space X a DBR subspace if its unit ball By admits farthest points from a dense set of points of X. In this paper, we study DBR subspaces of C(K). In the process, we study boundaries, in particular, the Choquet boundary of any general subspace of C(K). An infinite compact Hausdorff space K has no isolated point if and only if any finite co-dimensional subspace, in particular, any hyperplane is DBR in C(K). As a consequence, we show that a Banach space X is reflexive if and only if X is a DBR subspace of any superspace. As applications, we prove that any M-ideal or any closed *-subalgebra of C(K) is a DBR subspace of C(K). It follows that C(K) is ball remotal in C(K)**

An Integrated Effective Fragment—Polarizable Continuum Approach to Solvation: Theory and Application to Glycine

A new discrete/continuum solvation model has been developed by combining the effective fragment potential (EFP) for the discrete part and the polarizable continuum model (PCM) for the continuum part. The usefulness of this model is demonstrated by applying it to the calculation of the relative energies of the neutral and zwitterionic forms of glycine. These calculations were performed by treating glycine with ab initiowave functions. Water clusters were treated with bothab initio and EFP methods for comparison purposes, and the effect of the continuum was accounted for by the PCM model. The energy barrier connecting the zwitterionic and neutral three-water clusters was also examined. The computationally efficient EFP/PCM model gives results that are in close agreement with the much more expensive full ab initio/PCM calculation. The use of methods that account for electron correlation is necessary to obtain accurate relative energies for the isomers of glycine

Riboswitch Detection Using Profile Hidden Markov Models

<p>Abstract</p> <p>Background</p> <p>Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding. The sequence and structure of the aptamer domain is highly conserved in riboswitches belonging to the same class. We propose a method for fast and accurate identification of riboswitches using profile Hidden Markov Models (pHMM). Our method exploits the high degree of sequence conservation that characterizes the aptamer domain.</p> <p>Results</p> <p>Our method can detect riboswitches in genomic databases rapidly and accurately. Its sensitivity is comparable to the method based on the Covariance Model (CM). For six out of ten riboswitch classes, our method detects more than 99.5% of the candidates identified by the much slower CM method while being several hundred times faster. For three riboswitch classes, our method detects 97-99% of the candidates relative to the CM method. Our method works very well for those classes of riboswitches that are characterized by distinct and conserved sequence motifs.</p> <p>Conclusion</p> <p>Riboswitches play a crucial role in controlling the expression of several prokaryotic genes involved in metabolism and transport processes. As more and more new classes of riboswitches are being discovered, it is important to understand the patterns of their intra and inter genomic distribution. Understanding such patterns will enable us to better understand the evolutionary history of these genetic regulatory elements. However, a complete picture of the distribution pattern of riboswitches will emerge only after accurate identification of riboswitches across genomes. We believe that the riboswitch detection method developed in this paper will aid in that process. The significant advantage in terms of speed, of our pHMM-based approach over the method based on CM allows us to scan entire databases (rather than 5'UTRs only) in a relatively short period of time in order to accurately identify riboswitch candidates.</p

Unitaries in banach spaces

We study the abstract geometric notion of unitaries in a Banach space characterized in terms of the equivalence of the norm determined by the state space

A Combined Discrete/Continuum Solvation Model: Application to Glycine

A new solvation model that combines discrete and continuum descriptions of the solvent has been developed. The discrete solvent molecules are represented by effective fragment potentials (EFP), while the continuum is represented by the Onsager model. This (EFP+Onsager) model has been applied to the relative stabilities of the neutral and zwitterionic forms of glycine. Other supermolecule-continuum calculations were also performed, using quantum mechanical discrete waters and the isodensity polarizable continuum model (IPCM) or solvation model 5.42R (SM5.42R) for the continuum. It is shown that the Onsager model provides a poor description of the solvent in the supermolecule-continuum calculations. On the other hand, more sophisticated models can predict the correct energy order of the glycine isomers. Thus, the development of mixed methods that combine sophisticated continuum models with the discrete EFP model appear to be promising