GROMACS
Kushal Singh
Ph.D. Candidate
Bangalore
Summary
- Skilled Researcher enthusiastic about supporting advancements in computational biophysics. Passionate about increasing knowledge, adept at developing probing questions, designing experiments and generating meaningful results. Ready to apply knowledge and 6 years of experience in research. Experienced at identifying and using new technologies and resources. Works effectively and collaboratively with teams and individuals.
- Detail-oriented team player with strong organizational skills. Ability to handle multiple projects simultaneously with a high degree of accuracy.
- Proficient in performing experiments and assisting new students on research methods and data collection procedures. Skilled in conceptualization, design and implementation of projects.
Overview
10
10
years of professional experience
11
11
years of post-secondary education
Work History
Ph.D. Researcher
Solid State and Structural Chemistry Unit (SSCU), Indian Institute of Science (IISc)
Bangalore
01.2018 - Current
- Ph.D
- Research in computational biophysics under supervision of Professor Govardhan Reddy
- Topic of Research: Allosteric networks in proteins, biomolecular recognition processes, and ligand binding kinetics in protein/RNA systems
- Doctoral Thesis: An Exploration of Molecular Recognition Mechanisms and Ligand Induced Transitions in Biomolecules (Submitted)
- Developed research proposals, identified research objectives and created research plans in collaboration with leadership team to identify relevant questions in ligand binding processes in proteins/RNA and designed simulation protocols to address said questions.
- Analyzed and interpreted patterns and trends. Interpreted data analysis results to draw inferences and conclusions.
- Wrote research papers and reports addressing key questions in factors governing ligand binding processes in proteins/RNA.
Teaching Assistant, Computers in Chemistry
Indian Institute Of Science, Bangalore
Bangalore
01.2019 - 04.2019
- Teaching Assistant for the course 'Computers in Chemistry (CD224)'
- Assisted teachers with classroom management and document coordination to maintain positive learning environment.
- Supported classroom activities, tutoring, and reviewing work.
- Tutored struggling students individually and in small groups to reinforce learning concepts.
- Helped with grading assignments and tests, providing constructive feedback to students based on results.
Summer Intern
Indian Institute Of Science Education And Research, Thiruvananthapuram
Thiruvananthapuram
04.2015 - 07.2015
- Derived analytical expressions for band structures in graphyne using tight-binding models
- Completed research, compiled data, updated spreadsheets, and produced timely reports.
Summer Intern
Indian Institute Of Science Education And Research, Thiruvananthapuram
Thiruvananthapuram
05.2014 - 07.2014
- Assisted in developing novel NMR pulse sequences to identify cross couplings in organic molecules.
- Collaborated with senior Ph.D. students in research projects.
Education
Ph.D. - Chemistry
Indian Institute of Science (IISc)
Bangalore, Karnataka 01.2018 - 01.2024
BS-MS - Chemistry
Indian Institute of Science Education and Research, Thiruvananthapuram (IISER-TVM)
Thiruvananthapuram, Kerala 01.2012 - 01.2017
Skills
Python
undefinedResearch Interests
- Molecular Dynamics Simulations (Atomistic & Coarse-Grained)
- Allostery in Proteins
- RNA Dynamics
- Machine Learning in Simulations
- Ligand Binding Kinetics
- Computational Biophysics
Academic Awards
- Shyama Prasad Mukherjee Fellowship, Council of Scientific and Industrial Research (CSIR), Ministry of Science and Technology, Government of India, 2017, 2022, 14
- KVPY Fellow, Department of Science and Technology, Government of India, 2013, 2017
- INSPIRE Fellow, Department of Science and Technology, Government of India, 2012, 2013
Publications
- A. Gupta, K. Singh, Y. Patidar, R. Sharma, A.A. Sardesai, G. Reddy, B. Gopal, Allosteric Determinants in High Temperature Requirement A Enzymes are Conserved and Regulate the Population of Active Conformations, ACS Chemical Biology, 18, 7, 1487-1499, 2023
- K. Singh, A.N. Muttathukattil, P.C. Singh, G. Reddy, pH Regulates Ligand Binding to an Enzyme Active Site by Modulating Intermediate Populations, The Journal of Physical Chemistry B, 126, 47, 9759-9770, 2022
- K. Singh, G. Reddy, Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding Through Both Conformational and Induced Fit Mechanisms, Journal of Chemical Theory and Computation, 20, 1, 421-435, 2024
- K. Singh, S. Kumar, G. Reddy, Molecular Mechanisms Underlying Ligand Selectivity by Mn2+ Riboswitches, Manuscript under preparation
Training
- Poster Presentation, How Does a Riboswitch Differentiate Between Mg2+ and its Experimental Mimic Mn2+ for Specific Binding?, 28th Annual RNA Society Meeting, Singapore, 2023
- Oral Presentation, pH Effects on the Ligand Binding Kinetics of an Enzyme, In-house Unit Day Symposium, SSCU, IISc
Software
NAMD
AMBER
Affiliations
- Student Member, Biophysical Society
- Student Member, RNA Society
References
- Govardhan Reddy, Associate Professor, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560 012, greddy@iisc.ac.in, +91 80 2293 3533
- Balasubramanian Gopal, Professor, Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560 012, bgopal@iisc.ac.in, +91 80 2293-3219
- Anshu Pandey, Associate Professor, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore - 560 012, anshup@iisc.ac.in, +91 80 2293 2070
- Sai G. Ramesh, Associate Professor, Inorganic and Physical Chemistry Department, Indian Institute of Science, Bangalore - 560 012, sairamesh@iisc.ac.in, +91 80 2293-3409
Timeline
Teaching Assistant, Computers in Chemistry
Indian Institute Of Science, Bangalore
01.2019 - 04.2019
Ph.D. Researcher
Solid State and Structural Chemistry Unit (SSCU), Indian Institute of Science (IISc)
01.2018 - Current
Ph.D. - Chemistry
Indian Institute of Science (IISc)
01.2018 - 01.2024
Summer Intern
Indian Institute Of Science Education And Research, Thiruvananthapuram
04.2015 - 07.2015
Summer Intern
Indian Institute Of Science Education And Research, Thiruvananthapuram
05.2014 - 07.2014
BS-MS - Chemistry
Indian Institute of Science Education and Research, Thiruvananthapuram (IISER-TVM)
01.2012 - 01.2017
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