Srinidhi
Computational Biochemical Engineering
Portfolio
Introduction
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Skills: Biochemical Methods, Algorithms, Statistics, Computational Chemistry / Biology, Mathematical Modeling, Process Design and Optimization.
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Research experience in Mathematical Modeling, Structural Biology, Systems Pharmacology, Medicinal Chemistry, and DFT.
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Technical Certifications: “Lean Six Sigma Black Belt Professional” from Six Sigma Global Institute. ‘Bioreactor operations’ from National Institute for Bioprocessing Research and Training, Dublin, Ireland.
Email me at srinidh2@buffalo.edu / msrinidhi2@gmail.com
| ORCID | ResearchGate | BlueSky |
Education
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M.E, Chemical Engineering The State University of New York at Buffalo (SUNY) August 2022 -
B.E, Biotechnology M. S. Ramaiah Institute of Technology February 2020 -
CeDiD: 22G6-XJHD-SOI8 (Sr) Credential
Skills | Keywords
- Keywords: Statistical programming, Data Mining, Bioprocess Modelling, Biostatistics, Mathematical Modelling, Computational Process Development (Optimization, Validation), Theoretical Biology and Chemistry (DFT).
- Tech Stack: UniSim, MATLAB, Python, SAS, MiniTab, Cytoscape, Super-pro designer, GAMESS (US), PyMol, PyRx, AutoDock, Discovery Studio, Cobra Toolbox, MS Office, SLURM Scripting.
- Libraries: NumPy, Pandas, SciPy, Matplotlib, FiPy, Multiprocessing, Openpyxl.
- Database: GTEx, LINCS-1000, SDTM, ADaM, CDISC
- Laboratory Techniques and Instrumentation: UV Spectrophotometer, Meso-scale discovery systems, Tecan liquid handling systems, Watson-LIMS, Pinnacle 21 Community, TrackWise-QMS.
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Technical Certifications: ‘Lean Six Sigma Black Belt Professional’ Certification offered by Six Sigma Global Institute Certificate ‘Bioreactor operations’ from National Institute for Bioprocessing Research and Training, Dublin, Ireland
Graduate Course Work
- Biochemical Engineering
- Six Sigma for Chemical Engineers
- In vivo Molecular Imaging
- Mathematics and Computation for Chemical Engineers
- Metabolic Engineering
- Transport Phenomena
- Bioprocess Modeling
Academic/Training/Research Experience
| University at Buffalo (SUNY) | Research, Education and Training University | Aug 2021 – Aug 2022 |
Role: Student Assistant [Grader]
- Course: CE-561 Applied Chemical Kinetics.
- Responsible for Grading Homework papers and organizing data using Microsoft Office.
Role: Graduate Research Student
- Underwent training to run, analyze and debug repositories like cmapM.
- Utilized the processors at the center for computational resources for running SLURM scripts on these repositories.
- Repurposed available code to calculate and plot correlations between tissue and gene types in the GTEx database.
Project: Identify the source of variability in the HSR dynamics among C. Elegans worms using mathematical modeling.
- Formulated ODE model and performed parameter estimation using MATLAB for the average worm.
- Used MATLAB functions like fmincon to simulate heat shock treatment from steady state to steady state and performed sensitivity analysis.
- Scaled the predicted data and used plots to visualize the fit with empirical data and computed error values.
Project: Mathematical modeling of Sarcopenia in a transgenic Mouse Model.
- Updated an existing reactive diffusion sarcopenia model for simulation in Python.
- Performed literature survey and gathered recently published parameters for an existing sarcopenia model.
- Simulated a reactive diffusion model with updated parameters using Fipy, Matplotlib, Multiprocessing and OpenpyXL.
- Simulated the model for a five-year duration and plotted the variation of muscle length and mutant v/s wild type mtDNA.
- Performed and plotted sensitivity analysis on the model by varying parameters at discrete intervals.
Project: Optimization of methanol production in UNISIM by using the six sigma DMAIC methodology.
- Utilized plots (fishbone, run charts) to implement define and measure phase to assess initial process state.
- Pareto and residual plots were used to implement analyze and improve phases and visualize production rates.
- hypothesis testing indicated a significant increase in production (p<= 0.05).
- Implemented Control phase using contour plots and narrowed the ranges of parameters for increased yield.
- Checked for special cause variations during the optimization for preventing errors.
Project: A Novel gas generating nanoparticle ultrasound contrast agent for imaging neuronal COMT polymorphs.
- Yeast surface display and phage display protocols were mined from literature for designing possible candidate agents.
- Gathered, curated and presented possible protocols for invitro binding affinity tests and for synthesizing designed agents.
- Gathered, curated and presented possible protocols for testing these candidates in transgenic mice models.
- Proposed an alternate strategy for achieving the same result.
| The University of Trans Disciplinary Health Sciences and Technology | Research, Education and Training University | July 2019 – October 2019 |
Role: Research Intern
Project: Network Pharmacology Integrated Pharmacokinetics Approach to Decipher the Mechanism of Shankhapushpi Exerted Nootropic Activity
- Resolved the ambiguity regarding the original and most potent source among the four Shankhapushpi herbs by using a systems’ pharmacology and gene ontology approach.
- Curated the complete chemical space of the Shankhapushpi plants and established their impact of perturbation in the human model based on network statistics and predicted levels of resultant anxiolysis and long-term neuronal potentiation.
Project: Comparative Insilico Studies on Phytochemicals of Ocimum as Natural Inhibitors of Ebola VP-35 Protein
- Visualized the Ebola proteome and identified potential multifunctional targets for drug design and discovery.
- Showcased the importance of comparative analysis of two docking software outputs and compared their scoring algorithms for estimating the reliability of the obtained results based on published literature.
- Proposed the idea and application of a supplementary therapeutic aid for rapid use during global viral pandemic outbreaks.
| Syngene International Limited | Contract / Clinical Research Organization | February 2019 – June 2019 |
Role: Research Intern (Undergraduate Project)
Project: Role of Matrix and Sample Storage on Accuracy and Precision Evaluation for Validation of Bio-analytical Pharmacokinetic Assays
- Analyzed the efficiency of analyte recovery from stability samples prepared from multi-matrices by subjecting them to (accuracy, precision and drift) validation runs on a freshly developed bioanalytical pharmacokinetic assay for an actual drug candidate. Participated in laboratory documentation audits.
- Devised and pitched an idea for a universal acceptance criterion for validation sample preparation for minimized resource Consumption.
| Azyme Bio-sciences Pvt Ltd | Research, Education and Training Institute | August 2018 - September 2018 |
Role: Research Intern
- Intensive skill training in Process design and optimization of DNA extraction techniques, Agarose gel electrophoresis, restriction digestion, ligation, Biotransformation of B. subtilis and E. coli, Gene regulation, and investigated the effects of Ultraviolet and IR radiation for prospecting beneficial nutritional mutants.
| Biozeen Pvt Ltd | Bioprocess and Scale up Solutions | June 2018 - July 2018 |
Role: Industrial Trainee
- Biomass production of P. Pastoris in multimodal bioreactor assemblies. Performed routine EVSIP, FVSIP, CIP of production scale bioreactor installations along with cell culture techniques like media preparation, staining, sub-culturing and sketching piping and instrumentation diagrams of production scale process equipment tailored to the URS.
Preprints and Publications
- Srinidhi, “A Three-Pronged Computational Approach for Evaluating Density Based Semi Empirical Equations of Supercritical Extraction Process and Data,” Chemrxiv, 2024, [Doi] [PDF].
- Srinidhi, “Quantum chemical studies and pharmacophore modeling for designing novel keap1 antagonists that enhance nrf2 mediated neuroprotection,” African Journal of Biological Sciences, vol. 3, no. 2, pp. 130–156, 2021, [Url] [PDF].
- Srinidhi, “Artificial Neural Network (FFBP-ANN) Based Grey Relational Analysis for Modeling Dyestuff Solubility in Supercritical CO2 with Ethanol as the Co-Solvent,” Chemical Review and Letters, vol. 5, pp. 141–152, 2021, [Doi] [PDF].
- Srinidhi, “Network Pharmacology Integrated Pharmacokinetics Approach to Decipher the Mechanism of Shankhapushpi Exerted Nootropic Activity,” American Journal of Pharmacological Sciences, vol. 7, no. 1, pp. 25–38, Jan. 2019, [Url] [PDF].
- Srinidhi, “Comparative Insilico Studies on Phytochemicals of Ocimum as Natural Inhibitors of Ebola VP-35 Protein,” Indo-American Journal of Pharmaceutical Research, vol. 10, no. 10, 2019, [Doi] [PDF].