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.
Multilevel modeling of neurobiological systems in health and disease using combined imperative and declarative computational modeling approaches. Current research foci inlcude the molecular and cellular systems underlying Alzheimer Disease, depression, and eating disorders.
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
Systems biology, noise biology, viral and genetic circuitry, HIV, cellular fate-determination and state transitions, drug screening, gene regulation, single-cell biophysics
Our lab is interested in the study of the structure-function of membrane proteins involved in the metabolism of omega-3 and omega-6 fatty acids. Our main tools are nanodisc technology, targeted lipidomics, fluorescence spectroscopy, stopped flow spectroscopy, electrochemistry and protein engineering.
My research is in virus biophysics. Specifically, we investigate how physical forces control viral infectious cycles. Since physical forces are often more universal than specific biochemical molecular interactions, this knowledge helps us to understand not just how one type of virus works but how many classes of viruses replicate, providing insight into virus evolution and how to interfere with viral infections in a novel “biophysical” way.
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.
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; 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
The Kuehn lab studies microbial ecology and evolution using model organisms in the laboratory
Molecular Mechanisms of Cell Adhesion; Cell Engineering; Molecular force movements; structure; proteins; electrostatics; biomembranes
Gene circuits design and construction; mathematical modeling of bacterial gene regulation; development of synthetic microbial consortia; probiotic bacteria for therapeutic applications.
Rational design and directed evolution of proteins and catalytic DNA/RNAs and their applications in biocatalysis, sensing, imaging and drug delivery.
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.
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.
The Procko lab combines molecular evolution with deep sequencing to determine the fitness landscapes of mammalian transmembrane proteins.
Fundamental studies of biomolecular structure and dynamics. Interactions of lipids, proteins and drugs. NMR technology development, including experimental and computational methods. Applications to Parkinson’s disease, blood clotting disorders, and systemic fungal infections.
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.
Understanding behavior of key cellular signaling proteins involved in cancer for drug design & development; stress and energy signaling enzymes in plants, etc.
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.
Computational models of gene regulatory sequences and their evolution
Structure-function relationships in protein and nucleic acid systems
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
Development of imaging and optogenetic methods to delineate molecular mechanisms underlying cell fate determination; analysis of disrupted protein trafficking in neurodegenerative disorders.
Extreme/non-equilibrium properties of liquids; Glassy, jammed, and kinetically trapped soft matter; Self-healing soft robotics; Long timescale phenomena and rare events; Theory-driven atomistic simulations; Neutron and X-ray experiments
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