An Algorithmic Approach to the Identification of Rigid Domains in Proteins

Many proteins undergo conformational changes to perform their functions. A simple mechanism of conformational change in proteins is a rigid domain motion, in which two parts of a structure move rigidly with respect to each other. The identification of rigid domains is therefore useful in understanding the structure-function relationship of proteins. Many algorithms, including those in [16], [22], [13], [10], and [19], have been developed to identify rigid domains. In this paper we complement these works by proposing a mathematical definition of a rigid domain. We argue that our definition more accurately captures the intuitive notion of rigid domain in the previous work, than the quantitative definition of a rigid domain introduced by Nichols et al. [19]. Furthermore, our definition admits a practical approximation algorithm. We can prove theoretical guarantee on the quality of the output of our algorithm. We implement a randomized version of our algorithm, and demonstrate its effectiveness on several known protein complexes.     

Kinetics of the Kreis test through response surface methodology

The Kreis test is one of the procedures for early detection of oxidative products of fats and oils. The reaction is complicated, sensitive and continuous. The kinetics of the Kreis test have been studied as a function of reagent, phloroglucinol, oil quantity and incubation period for three oils with different fatty acid profiles, storage life and presence of compounds other than triglycerides. A central composite rotatable design with each factor at five levels required 20 experiments for each oil. The results of experiments carried out in duplicate have been examined by analysis of variance, and polynomials of appropriate degree were fitted to the data. The polyhedron search method was used to compute optimum conditions for carrying out the test for each oil. Three-dimensional graphs were generated to bring out the differences in the oils and the kinetics for each oil. Though “compromised” optimized conditions have been reported, the results indicate the necessity of more detailed investigation into the reaction.     

PSO Based Multi-Objective Approach for Controlling PID Controller

CSTR (Continuous stirred tank reactor) is employed in process control and chemical industries to improve response characteristics and system efficiency. It has a highly nonlinear characteristic that includes complexities in its control and design. Dynamic performance is compassionate to change in system parameters which need more effort for planning a significant controller for CSTR. The reactor temperature changes in either direction from the defined reference value. It is important to note that the intensity of chemical actions inside the CSTR is dependent on the various levels of temperature, and deviation from reference values may cause degradation of biomass quality. Design and implementation of an appropriate adaptive controller for such a nonlinear system are essential. In this paper, a conventional Proportional Integral Derivative (PID) controller is designed. The conventional techniques to deal with constraints suffer severe limitations like it has fixed controller parameters. Hence, A novel method is applied for computing the PID controller parameters using a swarm algorithm that overcomes the conventional controller's limitation. In the proposed technique, PID parameters are tuned by Particle Swarm Optimization (PSO). It is not easy to choose the suitable objective function to design a PID controller using PSO to get an optimal response. In this article, a multi-objective function is proposed for PSO based controller design of CSTR.     

MCU based real-time temperature control system for universal microfluidic PCR chip

The analysis of genetic materials in the post-human genome project era has become an ever-expanding branch of research and thus routinely employed in majority of biochemical laboratories. Most of the diagnostic research area emphasizes on polymerase chain reaction for detecting pathogenic organisms. However, the conventional polymerase chain reaction requires expensive and sophisticated thermal cycler and is not handy owing to its large dimensions. Therefore, we fabricated a continuous-flow polymerase chain reaction chip on a PDMS based microfluidic platform to ease the hardship of the conventional system. Temperature being the most crucial factor in polymerase chain reaction, was monitored and regulated by thermostatic action using an on-line computer system. Indium tin oxide coated glass platform was used for heating as it is transparent and has good thermal conductivity under the influence of DC bias. The heating circuit used an ATMega 128 MCU to control the temperature. As a result, a precise and quick heating environment was maintained on the microfluidic chip to amplify the target DNA. We successfully amplified Lambda phage and Escherichia coli DNA on our chip to prove the practicality of the device.     

Quantifying the effect of soil organic matter on indigenous soil N supply and wheat productivity in semiarid sub-tropical India

A field experiment was conducted on a loamy sand soil for six years to quantify the effect of soil organic matter on indigenous soil N supply and productivity of irrigated wheat in semiarid sub-tropical India. The experiment was conducted by applying different combinations of fertilizer N (0–180 kg N ha⁻¹), P (0–39 kg P ha⁻¹) and K (0–60 kg K ha⁻¹) to wheat each year. For the data pooled over years, fertilizer N together with soil organic carbon (SOC) and their interaction accounted for 75% variation in wheat yield. The amount of fertilizer N required to attain a yield goal decreased as the SOC concentration increased indicating enhanced indigenous soil N supply with an increase in SOC concentration. Besides SOC concentration, the soil N supply also depended on yield goal. For a yield goal of 4 tons ha⁻¹, each ton of SOC in the 15 cm plough layer contributed 4.75 kg N ha⁻¹ towards indigenous soil N supply. An increase in the soil N supply with increase in SOC resulted in enhanced wheat productivity. The contribution of 1 ton SOC ha⁻¹ to wheat productivity ranged from 15 to 33 kg ha⁻¹ across SOC concentration ranging from 3 to 9 g kg^-1 soil. The wheat productivity per ton of organic carbon declined curvilinearly as the native SOC concentration increased. The change in wheat productivity with SOC concentration shows that the effect of additional C sequestration on wheat productivity will depend on the existing SOC concentration, being higher in low SOC soils. Therefore, it will be more beneficial to sequester C in soils with low SOC than with relatively greater SOC concentration. In situations where the availability of organic resources for recycling is limited, their application may be preferred in soils with low SOC concentration. The results show that an increase in C sequestration will result in enhanced wheat productivity but the increase will depend on the amount of fertilizer applied and the existing fertility level of the soil.