The set of interacting molecules representing a biological pathway or network is a central concept in biology. It is within the pathway context that the functioning of individual molecules acquires purpose and it is the integration of these molecular circuitries that underlies the functioning of biological systems. In order to provide the research community with a dynamic platform for accessing...

7.2 Research Activities 7.2.1 Development of original molecular theory An atomicand molecular-level understanding of drug actions and the mechanisms of a variety of chemical reactions will provide insight for developing new drugs and materials. Although a number of diverse experimental methods have been developed, it still remains difficult to investigate the state of complex molecules and to f...

Maintaining a moving mesh of a deforming surface is widely studied in various disciplines. However, difficulties arise with requirements of topology changes, homeomorphism between mesh and surface, and guarantees of triangle quality. We propose a mesh deformation algorithm to satisfy the above requirements. We employ the skin surface by Edelsbrunner that approximates objects in fields like comp...

A special and important task in medicinal implant technology is to prevent the material from fouling or make it compatible for tissues by coating the material with functionalized lipid biomolecules. In order to rationalize the design of such new materials structural information about the film is needed. In this presentation we give an account on the investigation of coating of the tetraetherlip...

The present issue of the Journal of Computational Methods in Science and Engineering (JCMSE) is especially devoted to the II Congreso de Fisicoquı́mica Teórica y Computacional (II Congress of Theoretical and Computational Physical-Chemistry) (II CFQTC). This Congress took place at Choronı́, Venezuela, December 2–4 of 2008. II CFTC has considered different areas of general interest: molecular mode...

Electron diffraction is a valuable tool to capture structural information from molecules in the gas phase. However, the information contained in the diffraction patterns is limited due to the random orientation of the molecules. Additional structural information can be retrieved if the molecules are aligned. Molecules can be impulsively aligned with femtosecond laser pulses, producing a transie...

Single-cell RNA sequencing (scRNA-Seq) is a revolutionary technology, which allows studying fundamental biological questions that were previously out of reach [1, 2]. It allows, for the first time, to reveal a cell’s identity and characterize its molecular circuitry in an unbiased, data-driven way. The product of a scRNA-Seq experiment is a data matrix X where entry Xng approximates the number ...

We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we provide a comparison with related approaches and some hints for future extensions.

2-1 Volume Three FORMATION AND STABILITY OF SUBSTITUTED PYROMORPHITE: A MOLECULAR MODELING STUDY Abhijit V. Shevade, Larry Erickson, Gary Pierzynski, and Shaoyi Jiang Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506; Phone: 785-532-5584; Fax: 785-532-7372; Department of Agronomy, Kansas State University, Manhattan, KS 66506; Phone: 785-532-7209; Fax: 785-532-6094.