Faculty

Understanding how the remarkable functionality of biological nanomachines comes about from the spatial arrangement of their atoms and using this knowledge to design synthetic systems that exceed in the performance of their biological counterparts is the focus of this group's research program.

Single-molecule biophysics, quantum sensing, microscopy

Our research focuses on basic questions regarding how chromatin folds into interphase and mitotic chromosomes, how chromosomes are organized and move, in some cases over long distances, within interphase nuclei, and how chromosome organization and dynamics impact DNA functions such as transcriptional activation.

Experimental biological physics, high-resolution optical tweezers, molecular motors, nucleic acid and protein translocases

We are interested in how the lipids of a membrane regulate the function of membrane proteins such as SNAREs, Rab GTPases and ABC transporters.

Mechanisms of enzyme-catalyzed reactions, functional genomics, lignin deconstruction for biofuel production: the importance of chemistry in the evolution of new enzymatic activities

Examining the way living cells process information from their environment and make decisions based on that information. The aim is to form a quantitative narrative for the dynamics of cellular decision-making and unveil simple principles that underlie this process.

My laboratory is broadly interested in the relationship between structure and function in neurotransmitter-gated ion channels, with special emphasis on the Cys-loop superfamily of synaptic receptor-channels. Our main tools are single-channel and ensemble electrophysiology, and protein-engineering techniques.

Fast protein folding dynamics in vitro and in vivo studied by laser-induced temperature jump and pressure jump experiments and modeling; zebrafish and bacterial swimming behavior; protein-RNA interactions in live cells.

Unveiling the fundamental rules governing the ensemble behavior of complex biological systems; Spatially resolved integrative transcriptomics; Single virus genomics; High throughput, single-molecule resolution imaging; Microfluidics-based high throughput assays

Computational and structure-based design of enzyme inhibitors; explorations of small molecule-RNA binding

We are pursuing the molecular understanding of translation and its regulation using biochemical, genomic, and biophysical methods with an emphasis on macromolecule crystallography.

Application of single-molecule microscopy to study gene expression in vitro and in vivo; and DNA supercoiling and transcription; spatial organization of gene expression inside a single bacterial cell

Design of bioinspired materials, design of synthetic extracellular matrix; engineering of stem cell niches, FRET analysis of cell-ECM interaction; FRET analysis of biomolecular interaction; vascular/bone tissue engineering

Development of chemical imaging techniques to visualize the distribution of different components in cell membranes, and to understand how cell membrane structure and composition relates to disease progression

Molecular Mechanisms of Cell Adhesion; Cell Engineering; Molecular force movements; structure; proteins; electrostatics; biomembranes

Label-free quantitative phase imaging, super-resolution fluorescence microscopy, and multiscale spatial omics to study cancer initiation and drug resistance

Gene circuits design and construction; mathematical modeling of bacterial gene regulation; development of synthetic microbial consortia; probiotic bacteria for therapeutic applications.

Signalling Networks in Protein: RNA Complexes; Protein: Protein and Protein: RNA Docking; Course-Grained Models of in vivo Cell Processes; Origins of the Genetic Code; Evolution of Translation; and VMD/MultiSeq: Evolutionary Analysis Software

Molecular mechanisms of aminoacyl-tRNA synthetases and group I intron splicing; fidelity of protein synthesis

I work on evolutionary and systems biology and carry out computational modeling of complex biological systems ranging from genome evolution and biomolecular networks to ecosystem dynamics. I am a statistical physicist by training so that in my research I often use physics-based modeling techniques. I particularly love simple-yet-rich "bottom down" models.

X-ray crystallography, enzymology, DNA replication

Protein structure determination; design of novel drug molecules to kill parasitic protozoa causing malaria, sleeping sickness & opportunistic infections of immunocompromised individuals

The functions, evolutionary histories and structures of genes and proteins in Archaea

Preparing conformationally gated artificial metalloproteins and metallocofactors that mimic the way that biological systems use structural changes as a vehicle for the interconversion of different forms of energy. Exploring this mechanistic paradigm, applications include solar fuels conversion, targeted drug delivery, photocatalysis, and the generation of smart materials.

Application and development of computational and theoretical methods to study biological macromolecules using frameworks of molecular dynamics, quantum chemistry, and molecular evolution. Current emphasis is on cell signaling, membrane-associated phenomena, membrane-protein interactions, and protein folding.

Our research focuses on understanding the role of replication initiators in DNA replication, repair and chromatin organization and how mutations in key replication factors lead to genomic instability resulting in developmental disorders and cancer. Our research also dives into the role of BEN-domain transcription factors in chromatin organization and cell proliferation.

The Procko lab combines molecular evolution with deep sequencing to determine the fitness landscapes of mammalian transmembrane proteins.

High-throughput Chromosome Conformation Capture (Hi-C), Chromosome Surgery, Genome Engineering, Micromanipulation, Super-resolution Microscopy (SIM and DNA-Paint MINFLUX nanoscopy), Live single-cell RNA-seq, Digital Chromosome Banding

Development of novel tools for single cell and biomolecule analysis, including, bio-inspired materials, hydrodynamic trapping, gene network dynamics, and synthetic biology

Use of novel forms of fluorescence, at both single-molecule and ensemble levels, to study actomyosin, ion channels, and other biomolecules

Measuring chemical transmitters released from vesicles in real-time. Synaptic chemical transmission. Single cell signaling. Electrophysiology. Alzheimer’s diseases. Developing nanoelectrodes and multiplexed analytical platform to study neurotransmission.

The long-term research goal of Shukla group is to combine theory, computation, and experiments to develop quantitative models of molecular processes relevant for health, energy and climate change. We integrate ideas from a wide range of disciplines and aim to investigate the functional role of the “Dynamics” in molecular processes.

Our laboratory's focus is the development, characterization, and application of DNA as a catalyst (enzyme).

The Sing lab uses statistical mechanics, coarse-grained molecular simulation, and field theory to understand the polymer physics of biological macromolecules. Specific areas of interest include the role of electrostatics and sequence on intrinsically disordered proteins and intracellular phase separation, the role of DNA elasticity and binding kinetics in DNA-protein interactions, and the conformation and dynamics of dense polymer solutions.

Investigating the assembly, structures and functions of mucosal antibodies to understand how they protect vertebrates from external factors and how they can be engineered to treat disease. Common techniques used in the lab include cryoelectron microscopy, X-ray crystallography, surface plasmon resonance and fluorescence microscopy.

Computational studies of transport of molecules across biological membrane; structure-function relationship of membrane channels and transporters; Lipid-mediated regulation of binding and function of peripheral proteins

Studying the evolutionary constraints and trajectories of influenza virus and antibodies by systematically mapping their sequence-structure-function relationships. Saturation mutagenesis; Deep sequencing; High-throughput methodologies; Structural biology; X-ray crystallography; Bioinformatics

Development of imaging and optogenetic methods to delineate molecular mechanisms underlying cell fate determination; analysis of disrupted protein trafficking in neurodegenerative disorders.

Development and application of synthetic biology tools to address society's most daunting challenges in human health and energy, and investigation of the fundamental aspects of enzyme catalysis, cell metabolism, and gene regulation