Sudipta Kumar Sinha
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View article: Analogue information processing in NF-κB gene regulatory system
Analogue information processing in NF-κB gene regulatory system Open
Nuclear factor-κB (NF-κB) participates in various cellular processes to encompass cell fate through differential gene expression, but the underlying molecular mechanism behind this phenomenon is still elusive. Two factors in this process c…
View article: BRIDGING THE GAP: ADDRESSING FACULTY SHORTAGES AND CAREER INTEREST IN PHASE I SUBJECTS UNDER THE COMPETENCY-BASED MEDICAL EDUCATION CURRICULUM
BRIDGING THE GAP: ADDRESSING FACULTY SHORTAGES AND CAREER INTEREST IN PHASE I SUBJECTS UNDER THE COMPETENCY-BASED MEDICAL EDUCATION CURRICULUM Open
Objectives: Recently introduced competency-based medical education (CBME) curriculum necessitates a heavy presence of ably trained medical educators. Contrarily, Phase I subjects are facing a severe shortage of faculty, piloting a double s…
View article: A novel approach to navigate the taxonomic hierarchy to address the Open-World Scenarios in Medicinal Plant Classification
A novel approach to navigate the taxonomic hierarchy to address the Open-World Scenarios in Medicinal Plant Classification Open
In this article, we propose a novel approach for plant hierarchical taxonomy classification by posing the problem as an open class problem. It is observed that existing methods for medicinal plant classification often fail to perform hiera…
View article: A general, robust framework for determining the key species that forewarns sudden transitions in biological circuits
A general, robust framework for determining the key species that forewarns sudden transitions in biological circuits Open
The Cdc2-cyclin B/Wee1 kinase system exhibits bistability due to mutual inhibition. We explore the direction of critical slowing down near a tipping point to reveal the key biochemical species to best detect an upcoming transition.
View article: Predicting p53-dependent cell transitions from thermodynamic models
Predicting p53-dependent cell transitions from thermodynamic models Open
A cell’s fate involves transitions among its various states, each defined by a distinct gene expression profile governed by the topology of gene regulatory networks, which are affected by 3D genome organization. Here, we develop thermodyna…
View article: The Blueprint of Logical Decisions in a NF-κB Signaling System
The Blueprint of Logical Decisions in a NF-κB Signaling System Open
Nearly identical cells can exhibit substantially different responses to the same stimulus that causes phenotype diversity. Such interplay between phenotype diversity and the architecture of regulatory circuits is crucial since it determine…
View article: Can local heating and molecular crowders disintegrate amyloid aggregates?
Can local heating and molecular crowders disintegrate amyloid aggregates? Open
The present study employs a blend of molecular dynamics simulations and a theoretical model to explore the potential disintegration mechanism of a matured Aβ octamer, aiming to offer a strategy to combat Alzheimer's disease.
View article: Advisory Committee
Advisory Committee Open
View article: Predicting p53-Dependent Cell Transitions From Thermodynamic Models
Predicting p53-Dependent Cell Transitions From Thermodynamic Models Open
Matlab codes containing Grand Canonical Monte Carlo (GCMC) simulation codes and theoretical codes to study the first-order phase transition behavior of a malignant cell to a normal healthy cell. In this work, we develop thermodynamic model…
View article: Predicting p53-Dependent Cell Transitions From Thermodynamic Models
Predicting p53-Dependent Cell Transitions From Thermodynamic Models Open
Matlab codes containing Grand Canonical Monte Carlo (GCMC) simulation codes and theoretical codes to study the first-order phase transition behavior of a malignant cell to a normal healthy cell. In this work, we develop thermodynamic model…
View article: Identifying critical transitions in complex diseases
Identifying critical transitions in complex diseases Open
View article: Combined electromechanically driven pulsating flow of nonlinear viscoelastic fluids in narrow confinements
Combined electromechanically driven pulsating flow of nonlinear viscoelastic fluids in narrow confinements Open
Controlled microscale transport is at the core of many scientific and technological advancements, including medical diagnostics, separation of biomolecules, etc., and often involves complex fluids. One of the challenges in this regard is t…
View article: Anticipating response function in gene regulatory networks
Anticipating response function in gene regulatory networks Open
The origin of an ordered genetic response of a complex and noisy biological cell is intimately related to the detailed mechanism of protein–DNA interactions present in a wide variety of gene regulatory (GR) systems. However, the quantitati…
View article: Effects of stochasticity and social norms on complex dynamics of fisheries
Effects of stochasticity and social norms on complex dynamics of fisheries Open
Recreational fishing is a highly socioecological process. Although recreational fisheries are self-regulating and resilient, changing anthropogenic pressure drives these fisheries to overharvest and collapse. Here, we evaluate the effect o…
View article: Anticipating the Novel Coronavirus Disease (COVID-19) Pandemic
Anticipating the Novel Coronavirus Disease (COVID-19) Pandemic Open
The COVID-19 outbreak was first declared an international public health, and it was later deemed a pandemic. In most countries, the COVID-19 incidence curve rises sharply over a short period of time, suggesting a transition from a disease-…
View article: Anticipating the novel coronavirus disease (COVID-19) pandemic
Anticipating the novel coronavirus disease (COVID-19) pandemic Open
COVID-19 outbreak has been declared as a public health emergency of international concern, and later as a pandemic. In most countries, the COVID-19 incidence curve rises sharply in a short period, suggesting a transition from a disease-fre…
View article: An Inherent Structural Difference Between Serine and Threonine Phosphorylation: Phosphothreonine Prefers an Ordered, Compact, Cyclic Conformation
An Inherent Structural Difference Between Serine and Threonine Phosphorylation: Phosphothreonine Prefers an Ordered, Compact, Cyclic Conformation Open
Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circ…
View article: Possible Role of BCG-Induced Trained Immunity to Reduce the Prevalence and Severity of COVID-19 in High-Risk Population
Possible Role of BCG-Induced Trained Immunity to Reduce the Prevalence and Severity of COVID-19 in High-Risk Population Open
In the last few months COVID-19 has been spreading unchecked to most of the countries of the world.While the impact has varied from one nation to the other and the differences attributed to various factors, universal BCG vaccination is tho…
View article: Anticipating critical transitions in epithelial–hybrid-mesenchymal cell-fate determination
Anticipating critical transitions in epithelial–hybrid-mesenchymal cell-fate determination Open
In the vicinity of a tipping point, critical transitions occur when small changes in an input condition cause sudden, large, and often irreversible changes in the state of a system. Many natural systems ranging from ecosystems to molecular…
View article: Anticipating critical transitions in epithelial-hybrid-mesenchymal cell-fate determination
Anticipating critical transitions in epithelial-hybrid-mesenchymal cell-fate determination Open
In the vicinity of a tipping point, critical transitions occur when small changes in an input condition causes sudden, large and often irreversible changes in the state of a system. Many natural systems ranging from ecosystems to molecular…
View article: A charge equilibration formalism for treating charge transfer effects in MD simulations: Application to water clusters
A charge equilibration formalism for treating charge transfer effects in MD simulations: Application to water clusters Open
Conventional classical force fields by construction do not explicitly partition intermolecular interactions to include polarization and charge transfer effects, whereas fully quantum mechanical treatments allow a means to effect this disse…
View article: CCDC 1416011: Experimental Crystal Structure Determination
CCDC 1416011: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1416012: Experimental Crystal Structure Determination
CCDC 1416012: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 1416010: Experimental Crystal Structure Determination
CCDC 1416010: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …