GR-267 Churn Prediction

Employee churn is a situation where people leave the organization voluntarily or involuntarily. This has become a serious problem in recent times. We have also seen that attrition rates in several industries are going high. So, it is very much required to understand and analyze the reason behind attrition and why this is happening. We must conduct an analysis to know what the factors affecting employee churn are. It will create a huge impact on the organization if the attrition rate goes high. In order to resolve this issue, we are trying to take up this issue and find the best solution for this

Energetics of Actophorin revealed using Adaptive Steered Molecular Dynamics

Actin molecules are responsible for formation of actin filaments. These filaments provide the internal structure of the cell and are responsible for cellular motility through the process of actin threadmilling. Several accessory proteins are involved in the threadmilling process. In this thesis, I focus on one of these proteins called Actophorin. Wildtype Actophorin is extracted from Acanthamoeba castellani. Quirk and coworkers have introduced 19 site specific mutations in wildtype Actophorin. They found that these mutations have enabled the mutant Actophorin to display higher chemical and thermal stability compared to the wildtype. This was found by performing chemical denaturation studies. Free energy difference calculation at the transition midpoint from the denaturation studies reveal the mutant is more stable than the wildtype by 6.97 kCal/mol. Thermodynamic and kinetic properties from denaturation experiments can be correlated with atomic level interactions observed from Steered Molecular Dynamic (SMD) simulations of protein unfolding. This is done by measuring the Potential of Mean Force (PMF) of unfolding. When obtaining the PMF of unfolding of large proteins, SMD is inefficient as large proteins require large solvent boxes and convergence of PMF requires large amount of simulations. The Adaptive Steered Molecular Dynamics (ASMD) method method developed by Hernandez and coworkers overcomes these limitations by steering of the particle in stages allowing for convergence of the PMF using fewer trajectories compared to SMD. The telescoping water box method has also been introduced within ASMD to reduce the number of waters needed at each stage. That is, instead of having a large fixed size water box, the box gradually increases in size after every stage. The PMF obtained from ASMD shows that the work of unfolding for the mutant is higher than the wildtype by approximately 120 kCal/mol thus correlating well with the increased stability seen from denaturation experiments. Plots of number of hydrogen bonds, salt bridges and fraction of native contacts that remain after each stage of pulling provide insight on the trend observed in the PMF of mutant and wildtype Actophorin. ASMD was also used to study the effect on the PMF while pulling from two different ends of the protein. In one set of ASMD simulations the wildtype Actophorin was pulled from the C terminus end keeping the N terminus fixed. This is called as the “unflipped” Actophorin. In another set of ASMD simulation the N terminus was pulled keeping the C terminus fixed. This is called as “flipped” Actophorin. ASMD simulations show that the PMF obtained from both “flipped” and“unflipped” Actophorin correlate well indicating that the PMF is independent of which terminus is chosen to be the steered or fixed end

A Stoichiometric and Pseudo Kinetic Model of Loop Mediated Isothermal Amplification

Loop mediated isothermal amplification (LAMP) is one of the most popular isothermal DNA amplification techniques for research and commercial applications. The LAMP mechanism is powered by strategic primer design and a strand displacement polymerase, generating products that fold over, creating loops. LAMP leads to generation of products of increasing length over time. These products containing multiple loops are conventionally called cauliflower structures. Existing literature on LAMP provides extremely limited understanding of progression of cascades of reactions involved in the reaction and it is believed that cauliflower structures of increasing length constitute a majority of the product formed in LAMP. This study presents a first of its kind stoichiometric and pseudo kinetic model to comprehend LAMP reactions in deeper depth by (i) classifying LAMP reaction products into uniquely identifiable categories, (ii) generating a condensed reaction network to depict millions of interconnected reactions occurring during LAMP, and (iii) elucidating the pathways for amplicon generation. Despite the inherent limitations of conventional stoichiometric modelling for polymerization type reactions (the network rapidly becomes too large and intractable), our model provides new theoretical understanding of the LAMP reaction pathway. The model shows that while longer length products are formed, it is the smaller length recycle amplicons that contribute more towards the exponential increase in the amount of double stranded DNA. Prediction of concentration of different types of LAMP amplicons will also contribute substantially towards informing design of probe-based assays. </p

Implementation of telescoping boxes in adaptive steered molecular dynamics (ASMD)

Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics. The challenge has been the extraction of information from such simulations that generalize for complex nonequilibrium processes. The use of Jaryzinski\u27s equality opened the possibility of determining the free energy along the steered coordinate, but sampling over the nonequilibrium trajectories is slow to converge. Adaptive steered molecular dynamics (ASMD) and other related techniques have been introduced to overcome this challenge through the use of stages. Here, we take advantage of these stages to address the numerical cost that arises from the use of the very large solvent boxes required to simulate the entirety of the steered coordinate. We introduce a scheme, called a telescoping box, within ASMD in which we adjust the solvent box between stages, and thereby vary (and optimize) the required number of solvent molecules. We have benchmarked the method on a relatively long alpha-helical peptide, Ala30, with respect to the potential of mean force and hydrogen bonds. We show that the use of telescoping boxes introduces little numerical error while significantly reducing the computational cost