Soumen Bera
“Imagination is more important than knowledge.” - Albert Einstein
My primary research Aims to achieve scientific breakthrough and develop innovative methods, model and technics to better understand biological systems using interdisciplinary approaches from Applied Mathematics, Biochemistry, Biophysics and Bioinformatics. The implication of my results will be in drug discovery, medicine, protein science and biological data science.
Research Projects
Past projects
Integrative structural modelling:
Essential Biological Process are carried out by macromolecular assembly and it is important to know the structure and its components and how they interacting to each other. However, by direct experimental method is difficult to predict the functions of macromolecular assembly and its components as lack of universal experimental method. In my PhD project, I try to understand the conformational dynamics and Allosteric regulation of hexameric Glutamate Dehydrogenase (GDH) using rigidity theory (Graph theory and Pebble game algorithm), Molecular Dynamics simulation, Normal Mode Analysis and Bioinformatics. Another project (Dual affinity role of nitrate transporter upon nitrate binding establishes phosphorylated/non-phosphorylated states), I have developed small method to understand the protein flexibility upon random mutation which facilitates Allosteric communication between two different sites. My focus also in Artificial Intelligence (AI) as a tool to better understand the molecular mechanism of macromolecular assembly.
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Bera et al., 2020 (Nature Scientific Reports)
Rashid & Bera et al., 2020 (Biophysical Journal)
Network motif in Biology:
From cell differentiation to signal transaction, Gene regulatory network play a crucial role within every process of life. The dynamics of network can shed light to understand the mechanism of disease which is occured by dysregulation of cellular process. Mathematical model with the combination of logic functions (e.g. “and” function, “switch” function, “or” function) can be beautifully preserved the dynamics of this network and predict the specific behavior of network.
I have also involved another project on “Reorganization of Nitrogen biogeochemical pathways upon fluctuating soil redox conditions” where we have shown the Bistability in-between Nitrogen source (x) and Nitrogen sink (y) subsystems interconnection with positive feedback loop and microbial genomics.
Mathematical and Kinetics Modelling:
Hyperinsulinism/hyperammonemia syndrome (HI/HA), the most common cause of recurrent hypoglycaemia in early infancy, is linked to glutamate dehydrogenase (GDH) activity as a regulator of insulin and ammonia homeostasis. However, it remains elusive what specific role GDH plays through its functional compartmentalization in the liver. Here we address this question by combining mathematical modelling, numerical simulation and enzyme kinetics and bioinformatics.
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Development Methods and technics in Biology:
Building a meaningful biological model, extracting important information and predicting hypothesis that are consisting with available myriad data is one of the key challenges in Biology. My focus also development some method using this numerous data and statistics tools to predict or extract new information. Recently, I have developed small method to understand protein flexibility upon random mutations which is available in my IScience Paper.
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