Background: Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data. Methods: We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned. Results:The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans. Conclusions:We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. A webserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet.in/ms3align.

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In this paper, a decentralized dynamic sliding mode control (DySMC) strategy is applied to a multivariable level control system. The time derivative of the control input of the DySMC is considered a new control variable for an augmented system which is composed of the original system and the integrator. This DySMC can transfer discontinuous terms to the first-order derivative of the control input and effectively reduce the chattering. The interactions between input/output variables are a common phenomenon and a challenging task in the design of multi-loop controllers for interacting multivariable processes. For reducing the interaction among variables, ideal decouplers are used. Independent diagonal controllers are designed for each decoupled subsystem, which is reduced to the first-order plus dead-time (FOPDT) model. A numerical simulation test has been carried out on a reactor system of the Industrial-Scale Polymerization (ISP). Experimental tests are performed to check the efficacy of the proposed controller using a laboratory-level coupled tank system.  A comparison of the proposed approach and sliding mode controller (SMC) is presented. Simulation and experiment results show that the DySMC approach reduces the chattering, and compensates for the effect of the external disturbances, and parametric uncertainties.

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