G. Reddy

Adaptive algorithms for shaping behavior

This paper develops a machine learning framework for shaping animal behavior using adaptive algorithms that alternate between simpler and harder tasks to optimize learning.

Inferring sparse structure in genotype-phenotype maps

This paper introduces a method to infer sparse structure in genotype-phenotype maps by identifying core processes that influence multiple phenotypes and genetic loci.

Local RNA Structure, Ion Hydration Shell and the Energy Barrier for Water Exchange from the Ion Hydration Shell Determine the Mechanism of Ion Condensation on Specific RNA Sites

The paper investigates how local RNA structure, ion hydration shell arrangement, and energy barriers influence metal ion binding to RNA, focusing on a riboswitch aptamer domain.

pH Effect on Ligand Binding to an Enzyme Active Site

This study uses simulations to investigate how pH affects guanidinium ion binding to the active site of hen-egg white lysozyme, revealing key binding pathways and the role of protonation states.

pH Induced Switch in the Conformational Ensemble of an Intrinsically Disordered Protein Prothymosin-α and Its Implications to Amyloid Fibril Formation

This study investigates how pH changes affect the conformational ensemble of the intrinsically disordered protein prothymosin-α and its role in amyloid fibril formation.

Mechanism of Mg2+ Mediated Encapsulation of an Anionic Cognate Ligand in a Bacterial Riboswitch

This paper investigates the mechanism of Mg2+ mediated encapsulation of an anionic ligand in a bacterial riboswitch using computational simulations.

A reinforcement-based mechanism for discontinuous learning

This paper shows that biologically-plausible reinforcement learning rules with persistent exploration can produce discontinuous learning in structured environments, explaining sudden insight during navigation tasks.

Salt Induced Transitions in the Conformational Ensembles of Intrinsically Disordered Proteins

The paper studies salt-induced conformational changes in intrinsically disordered proteins using simulations and experimental data, finding salt-specific effects depend on protein class and salt type.

Alternation emerges as a multi-modal strategy for turbulent odor navigation

The paper shows that alternation, a behavior in foraging mammals, is a multi-modal strategy for navigating turbulent odor plumes, combining casting, surging, and decision-making under partial observability.

Riboswitch Folds to Holo-Form Like Structure Even in the Absence of Cognate Ligand at High Mg2+ Concentration

The paper investigates whether riboswitches can form holo-form like structures without their cognate ligand at high Mg2+ concentrations using simulations.

Energy Landscape of Ubiquitin is Weakly Multidimensional

The paper investigates the energy landscape of ubiquitin using simulations, finding it weakly multidimensional with a single dominant barrier and a force-dependent transition state location.

Sector search strategies for odor trail tracking

This study develops an optimization framework to explain odor trail tracking behavior in animals, showing how search geometry limits tracking speed and when casting is necessary.

Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

This paper uses simulations to show that nucleosome unwrapping has asymmetric HPC rotation depending on force direction, explaining hysteresis in DNA stretching experiments.

A lexical approach for identifying behavioral action sequences

This paper introduces BASS, an algorithm that identifies rare behavioral action sequences in sequential data, demonstrating its effectiveness in zebrafish and glider simulations.

Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation

This study identifies double domain swapping as a mechanism driving early aggregation in human γC and γD crystallin proteins through molecular dynamics simulations.

Global epistasis emerges from a generic model of a complex trait

The paper shows that global epistasis patterns emerge from microscopic epistasis, confirming a quantitative relationship and introducing a new fitness landscape model.

Mg2+ Sensing by an RNA Fragment: Role of Mg2+ Coordinated Water Molecules

This study investigates how Mg2+ ions facilitate RNA folding through coordinated water molecules, showing that Mg2+ enables efficient folding while other ions like K+ and Ca2+ do not.

A Transient Intermediate Populated in Prion Folding Leads to Domain Swapping

This study identifies a transient intermediate state in prion folding that leads to domain swapping, suggesting a pathogenic mechanism for prion aggregation.

Zinc Solubilizing Plant Growth Promoting Microbes Produce Zinc Nanoparticles

The paper identifies plant growth promoting microbes that solubilize zinc and produce zinc nanoparticles, showing their size, stability, and biosynthesis mechanisms.

Role of Disulfide Bonds and Topological Frustration in the Kinetic Partitioning of Lysozyme Folding Pathways

This paper shows that two disulfide bonds in lysozyme cause a slow folding pathway by trapping the protein in an intermediate state, which disappears when the bonds are removed.

Cosolvent Effects on the Growth of Protein Aggregates Formed by a Single Domain Globular Protein and an Intrinsically Disordered Protein

This study investigates how cosolvents affect the growth of protein aggregates formed by a globular protein and an intrinsically disordered protein using simulations.

Universal nature of collapsibility in the context of protein folding and evolution

The paper resolves the SAXS-FRET controversy by showing that unfolded protein states are universally compact, with β-sheet-rich proteins being more collapsible, and suggests collapsibility constrains protein evolution.

Receptor crosstalk improves concentration sensing of multiple ligands

This study shows that receptor crosstalk can enhance precision in sensing multiple ligand concentrations by utilizing non-cognate ligand binding events.

Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin

This study uses molecular simulations to show that ubiquitin folding is preceded by collapse, resolving discrepancies between experimental methods.