Dr. Sheeba Malik

Dr. Sheeba Malik

Computational Biophysicist

Postdoctoral Research Fellow at Max Planck Institute for Dynamics of Complex Technical Systems, Germany

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About Me

Membrane simulation visualization

I am a computational biophysicist specializing in large-scale molecular dynamics simulations, high-performance computing, and theoretical modeling of complex molecular systems.

My research focuses on lipid membrane phase behavior, interfacial water thermodynamics, solvent-biopolymer interactions, and transport phenomena in biological and biomass-derived materials.

With experience as PI and Co-PI on NSF ACCESS allocations, I have led multi-million core-hour simulation campaigns and developed optimized GPU-accelerated workflows.

2
NSF Grants

Research Interests

Molecular Dynamics Simulations

Expert in all-atom simulations, coarse-grained modeling, umbrella sampling, and absolute binding free energy calculations.

High-Performance Computing

Proficient in job scheduling using SLURM, parallel processing, and workflow optimization for large-scale simulations.

Biophysical Systems

Specialized in interfacial water dynamics, phase transitions, lipid membranes, DNA, and cellulose dynamics.

Algorithm Development

Skilled in developing custom algorithms, data analysis, and statistical modeling for complex systems.

Machine Learning

Experience with ML techniques such as TensorFlow, Scikit-Learn, and Keras for data-driven analysis in computational chemistry.

Scientific Leadership

Demonstrated leadership in mentoring junior researchers, securing grants, and contributing to peer-reviewed publications.

Technical Skills

Simulation Tools

GROMACS CHARMM-GUI AMBER MDAnalysis LAMMPS NWChem Gaussian PLUMED OpenMM

Visualization Tools

PyMOL UCSF Chimera VMD ChemDraw Avogadro Blender OVITO

Programming Languages

Python FORTRAN Shell Script MATLAB C++ LaTeX

Machine Learning

TensorFlow Scikit-Learn Keras Jupyter Notebook

Selected Publications

Simulation and Generalized Langevin Equation Study of Lipid Subdiffusion in Biomembrane Phases

Malik, S., Kneller, G.R., Smith, M.D., Smith, J.C.

Biophysical Journal, 2025

Artificial Intelligence-Driven Aptamer Optimization Pipeline for Targeted Therapeutics in Healthcare

Gupta, T., Sharma, P., Malik, S., Pant, P.

Molecular Pharmaceutics, 2025

Relaxation time scales of interfacial water upon fluid to ripple to gel phase transitions of bilayers

Malik, S., Karmakar, S., Debnath, A.

Journal of Chemical Physics, 2023, 158, 114503

Quantifying dynamical heterogeneity length scales of interface water across model membrane phase transitions

Malik, S., Karmakar, S., Debnath, A.

Journal of Chemical Physics, 2023, 158, 091103

Structural changes of interfacial water upon fluid-ripple-gel phase transitions of bilayers

Malik, S., Debnath, A.

Chemical Physics Letters, 2022, 799, 139613

Dehydration-induced ordering mechanism of lipid bilayers

Malik, S., Debnath, A.

Journal of Chemical Physics, 2021, 154, 174904

View All Publications on Google Scholar

Experience

Postdoctoral Research Fellow

Jan 2026 - Present

Max Planck Institute for Dynamics of Complex Technical Systems

Magdeburg, Germany

Advisor: Prof. Matthias Stein

Conducting computational research on ion-selective membrane systems, hardwood lignin behavior in solvents of varying concentrations, and norovirus protein structure, dynamics, and binding interactions. Also supervising one PhD student on a protein-related project.

Postdoctoral Research Fellow

May 2023 - Jan 2026

University of Tennessee & Oak Ridge National Laboratory

Tennessee, USA

Advisor: Prof. Jeremy C. Smith

  • Designed and executed large-scale all-atom MD simulation campaigns (>1 million core-hours).
  • Developed GPU-optimized workflows in GROMACS, reducing simulation turnaround time by 30%.
  • Applied generalized Langevin equation modeling to characterize non-Markovian subdiffusive transport.
  • Led NSF ACCESS computational allocations as PI/Co-PI.

Ph.D. in Computational Biology

Jul 2017 - July 2022

Indian Institute of Technology (IIT) Jodhpur

Jodhpur, India

Advisor: Prof. Ananya Debnath

Thesis: "Dynamical Heterogeneity of Interface Water upon Membrane Phase Transitions"

Grants & Awards

NSF ACCESS Grant (Co-PI)

BIO240114 | Apr 2024 - Mar 2026

Combinatorial effects of ABE fermentation products on lipid membrane structure and organization.

NSF ACCESS Grant (PI)

BIO240046 | Feb 2024 - Mar 2026

Dynamical Influences on Co-solvent Phase Separation in Biomass for Bioenergy Applications.

UT Travel Award

Received to present work at Biophysical Conference 2025.

Senior Research Fellowship (MHRD)

Jul 2019 - Jul 2022

Awarded based on qualifying the GATE exam.

Get in Touch

Address

Max-Planck-Institute
Sandtorstraße 1
D-39106 Magdeburg
Germany

Connect with Me

Google Scholar GitHub ORCID

"Advancing molecular-level understanding of structure-dynamics relationships across biological and soft-matter systems"