U. Roy

Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity

This study identifies phosphate transporters in Candida albicans and shows how mutations in these genes affect growth and stress resistance under phosphate scarcity.

Spatio-temporal Pattern Formation due to Host-Circuit Interplay in Gene Expression Dynamics

The paper investigates spatio-temporal pattern formation in a cellular array with non-cooperative positive feedback, analyzing stability and spatial distribution under varying diffusion conditions.

Implications of Spike Protein Interactions with Zn-bound form of ACE2: A Computational Structural Study

This study investigates the impact of excluding a zinc ion from ACE2-S1 protein complex simulations, finding that Zn-bound complexes show greater stability and stronger binding free energy.

Molecular Investigations of Selected Spike Protein Mutations in SARS-CoV-2: Delta and Omicron Variants and Omicron Subvariants

The paper examines structural changes and mutation profiles in SARS-CoV-2 spike protein variants and subvariants to identify potential drug targets and neutralizing antibodies.

Ferric reductase-related proteins mediate fungal heme acquisition

The paper identifies Frp1 and Frp2 as proteins required for heme utilization in Candida albicans and shows they form a functional complex with CFEM hemophores for extracellular heme uptake.

Spatiotemporal patterning enabled by gene regulatory networks

The paper investigates how spatiotemporal patterns emerge from synthetic gene regulatory networks with diffusion in 1D and 2D space, analyzing stability and diffusion effects.

Lattice-based microenvironmental uncertainty driven phenotypic decision-making: a comparison with Notch-Delta-Jagged signaling

The paper develops a lattice-based agent model driven by microenvironmental uncertainty to study multicellular phenotypic decision-making, comparing it with Notch-Delta-Jagged signaling.

Structures of core eukaryotic protein complexes

The paper uses coevolution analysis and deep learning to model core eukaryotic protein complexes in yeast, identifying 104 new assemblies and structurally characterizing 608 previously unknown complexes.

Comparative Structural Analyses of Selected Spike Protein-RBD Mutations in SARS-CoV-2 Lineages

This paper computationally analyzes the structural changes in SARS-CoV-2 spike protein RBD mutations across multiple lineages to understand their implications for viral spread and pathogenicity.

Modeling Substrate Coordination to Zn-Bound Angiotensin Converting Enzyme 2

This study computationally designs Ang II mutants to identify strong ACE2 binders and examines their stability and binding energy using molecular dynamics simulations.

Intermediate adhesion maximizes fluidity and migration velocity of multicellular clusters

This study shows that intermediate cell-cell adhesion optimizes migration speed of multicellular clusters by balancing cohesion and fluidity.

Rad51 paralog complex Rad55-Rad57 acts as a molecular chaperone during homologous recombination

This study shows Rad55-Rad57 acts as a molecular chaperone in HR by facilitating Rad51 filament reassembly after Srs2 disruption.

Bypass of DNA Interstrand crosslinks by a Rev1-DNA polymerase ζ complex

This study shows that the Rev1-Pol ζ complex is more efficient than Pol ζ alone or Pol η in bypassing ICL damage, with Rev1's structural role being critical for TLS efficiency.

Ultrasensitivity and Fluctuations in the Barkai-Leibler Model of Chemotaxis Receptors in Escherichia coli

This paper analyzes a stochastic version of the Barkai-Leibler chemotaxis model in E. coli, showing ultrasensitivity and noise characteristics in receptor activity.