Faculty
- Daniel Palanker
- William Greenleaf
Our lab focuses on developing methods to probe the ... more - Surya Ganguli
- KC Huang
- Aaron Straight
- Jan M. Skotheim
- Jelena Vuckovic
- Vijay S. Pande
- Audrey K. Ellerbee
- W. E. Moerner
- Mark J. Schnitzer
- Stephen Quake
- Daniel S. Fisher
- Sebastian Doniach
- Philip H. Bucksbaum
- Steven M. Block
- Daniel Herschlag
- Olav Solgaard
- Hideo Mabuchi
Courses
- Theoretical Neuroscience
- Engineering Principles in Molecular Biology
- Physical Biology of Cells
- Advanced Cell Biology
- Advanced Molecular Biology
- Principles of Cell Cycle Control
- Physical Chemistry
- Physical Biology of Macromolecules
- Biology by the Numbers
- Stochastic and Nonlinear Dynamics
- Cellular Biophysics
- Introductory Biophysics
- Methods in Computational Biology
- Numerical Methods for Physicists and Engineers
- Neuronal Biophysics
- Photons, Biological Photosynthesis, and Quantum Mechanics
- Introduction to Photonics
- Chemistry of Biological Processes
- Advanced Imaging Lab in Biophysics
- Laboratory Electronics
- Biological Macromolecules
- Estimation and Control Methods for Applied Physics
Publications
- Optoelectronic retinal prosthesis: system design and performance
- Dynamics of Retinal Photocoagulation and Rupture
- Electrosurgery with Cellular Precision
- Strength-duration relationship for extracellular neural stimulation: numerical and analytical models
- Selective Retinal Therapy with Microsecond Exposures Using a Continuous Line Scanning Laser
- Improving the Therapeutic Window of Retinal Photocoagulation by Spatial and Temporal Modulation of the Laser Beam
- Photodiode Circuits for Retinal Prostheses
- Multi-Focal Laser Surgery: Cutting Enhancement by Hydrodynamic Interactions Between Cavitation Bubbles
- Femtosecond Laser–Assisted Cataract Surgery with Integrated Optical Coherence Tomography
- High-resolution, single-molecule measurements of biomolecular motion
- Artificial cavitation nuclei significantly enhance acoustically induced cell transfection
- Direct observation of basepair stepping by RNA polymerase
- Single-molecule, motion-based DNA sequencing using RNA polymerase
- An optical apparatus for rotation and trapping
- Fluorogenic DNA Sequencing in PDMS Microreactors
- Function Constrains Network Architecture and Dynamics: A Case Study on the Yeast Cell Cycle Network
- One Dimensional Dynamics of Attention and Decision Making in LIP
- Memory Traces in Dynamical Systems
- Feedforward to the past: the relation between neuronal connectivity, amplification, and short-term memory
- Statistical Mechanics of Compressed Sensing
- Short-term memory in neuronal networks through dynamical compressed sensing
- Dynamic structures in Escherichia coli: Spontaneous formation of MinE rings and MinD polar zones
- Pattern Formation within Escherichia coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules
- Min oscillations in round bacteria
- The Min system as a general cell-geometry detection mechanism: patterns of Min oscillations respond to changes in cell shape in aberrantly shaped Escherichia coli
- Dynamic SpoIIIE assembly mediates septal membrane fission during Bacillus subtilis sporulation
- A curvature-mediated mechanism for localization of lipids to bacterial poles
- Cooperative gating and spatial organization of membrane proteins through elastic interactions
- Lipid localization in bacterial cells through curvature-mediated microphase separation
- Macromolecules that prefer their membranes curvy
- Cell shape and cell-wall organization in Gram-negative bacteria
- Polo-like kinase controls vertebrate spindle elongation and cytokinesis
- Centromeric chromatin gets loaded
- Centromere formation: from epigenetics to self-assembly
- Fluorescent protein applications in microscopy
- Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation
- Centromere assembly requires the direct recognition of CENP-A nucleosomes by CENP-N
- Dissection of CENP-C-directed centromere and kinetochore assembly
- Image analysis benchmarking methods for high-content screen design
- Dual recognition of CENP-A nucleosomes is required for centromere assembly
- Local Geometry and Elasticity in Compact Chromatin Structure
- The effects of molecular noise and size control on variability in the budding yeast cell cycle
- Positive feedback of G1 cyclins ensures coherent cell cycle entry
- To divide or not to divide
- Daughter-specific transcription factors regulate cell size control in budding yeast
- Cell cycle analysis: Live-cell imaging
- Commitment to a cellular transition precedes genome-wide changes in transcription
- Distinct interactions are responsible for the selection of maintenance of a cell fate
- X-ray structure determination of the glycine cleavage system protein H of Mycobacterium tuberculosis using an inverse Compton synchrotron X-ray source
- Direct observation of hierarchical folding in single riboswitch aptamers
- Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime
- A Dozen Years of Single-Molecule Spectroscopy in Physics, Chemistry, and Biophysics
- Methods of Single-Molecule Fluorescence Spectroscopy and Microscopy
- Improving the Mismatch Between Light and Nanoscale Objects with Gold Bowtie Nanoantennas
- Suppressing Brownian Motion of Individual Biomolecules in Solution
- New Directions in Single-Molecule Imaging and Analysis
- The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation
- Inside the Chaperonin toolbox: Theoretical and computational models for chaperonin mechanism
- Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint
- Progress and Challenges in the Automated Construction of Markov State Models for Full Protein Systems
- Charge, hydrophobicity, and confined water: Putting past simulations into a simple theoretical framework
- Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
- Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models
- Protein folded states are kinetic hubs
- Bayesian inference for Brownian dynamics
- A Simple Theory of Protein Folding
- High-Throughput Sequencing of the Zebrafish Antibody Repertoire
- Rate of Adaptation in Large Sexual Populations
- The Rate at Which Asexual Populations Cross Fitness Valleys
- Evolutionary Dynamics
- The Speed of Evolution and Maintenance of Variation in Asexual Populations
- Ordered Phosphorylation Governs Oscillation of a Three-Protein Circadian Clock
- Slide-and-cluster models for spindle assembly
- Single-molecule fluorescence enhancements produced by a Bowtie nanoantenna
- Reconstruction Of Low-Resolution Three-Dimensional Density Maps From One-Dimensional Small-Angle X-Ray Solution Scattering Data For Biomolecules
- Simulation Of Protein Folding By Reaction Path Annealing
- Closing The Folding Chamber Of The Eukaryotic Chaperonin Requires The Transition State Of Atp Hydrolysis
- A Comparative Study Of Motor-Protein Motions By Using A Simple Elastic-Network Model
- Random-Coil Behavior And The Dimensions Of Chemically Unfolded Proteins (Vol 101, Pg 12491, 2004)
- Protein Misfolding And Amyloid Formation For The Peptide Gnnqqny From Yeast Prion Protein Sup35: Simulation By Reaction Path Annealing
- Evaluation Of Ion Binding To Dna Duplexes Using A Size-Modified Poisson-Boltzmann Theory
- Low-Resolution Models For Nucleic Acids From Small-Angle X-Ray Scattering With Applications To Electrostatic Modeling
- Minactionpath: Maximum Likelihood Trajectory For Large-Scale Structural Transitions In A Coarse-Grained Locally Harmonic Energy Landscape
- The Complete Vs Ribozyme In Solution Studied By Small-Angle X-Ray Scattering
- The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure
- In vivo brain imaging using a portable 3.9 gram two-photon fluorescence microendoscope
- Fiber-optic fluorescence imaging
- In vivo imaging of mammalian cochlear blood flow using fluorescence microendoscopy
- Fast-scanning two-photon fluorescence imaging based on a microelectromechanical systems two-dimensional scanning mirror
- Minimally invasive high-speed imaging of sarcomere contractile dynamics in mice and humans
- High-speed, miniaturized fluorescence microscopy in freely moving mice
- Motor behavior activates Bergmann glial networks
- In vivo fluorescence imaging with high-resolution microlenses
- Advances in light microscopy for neuroscience
- In vivo brain imaging using a portable 2.9 g two-photon microscope based on a microelectromechanical systems scanning mirror
- Automated analysis of cellular signals from large-scale calcium imaging data
- siRNA silencing of keratinocyte-specific GFP expression in a transgenic mouse skin model
- Micromirror-scanned dual-Axis confocal microscope utilizing a gradient-index relay lensfor image guidance during brain surgery
- Assessing delivery and quantifying efficacy of small interfering ribonucleic acid therapeutics in the skin using a dual-axis confocal microscope
- Spectral-domain phase microscopy
- Doppler flow imaging of cytoplasmic flow using spectral domain phase microscopy
- Phase retrieval in low-coherence interference microscopy
- Spectral domain phase microscopy for local measurements of cytoskeletal rheology in cells
- Investigating nanoscale cellular dynamics with cross-sectional spectral domain phase microscopy
- Direct observation of the binding state of the kinesin head to the microtubule
- Applied force reveals mechanistic and energetic details of transcription termination
- Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
- Single-molecule, motion-based DNA sequencing using RNA polymerase
- Sequence-resolved detection of pausing by single RNA polymerase molecules
- Passive all-optical force clamp for high-resolution laser trapping
- Statistical kinetics of macromolecular dynamics
- Direct observation of base-pair stepping by RNA polymerase
- Kinesin moves by an asymmetric hand-over-hand mechanism
- Force and velocity measured for single molecules of RNA polymerase
- Direct observation of kinesin stepping by optical trapping interferometry
- A Single Molecule Study of RNA Catalysis and Folding
- Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
- Direct Measurement of the Full, Sequence-dependent Folding Landscape of a Nucleic Acid
- Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
- Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
- Direct Measurement of Tertiary Contact Cooperativity in RNA Folding
- Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble
- Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active Site Metal Ion
- Origins of Catalysis by Computationally Designed Retroaldolase Enzymes
- Multiple Native States of an RNA Enzyme Reveal Persistent Ruggedness of an RNA Folding Landscape
- Quantum dot photon statistics measured by three-dimensional particle tracking
- Precise characterization of the conformation fluctuations of freely diffusing DNA: beyond Rouse and Zimm
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- Department of Biology
- Department of Bioengineering
- Department of Biochemistry
- Quantitative Biology @ Stanford
- Biophysics Program
- MEMS two-photon microscope / Schnitzer and Solgaard Labs
Mass of a MEMS two-photon microscope developed for ... more - Center for Biological Imaging at Stanford
- Molecular Imaging Program at Stanford
- Bio-X
- Stanford Synchrotron Radiation Lightsource (SSRL)
- Stanford Photonics Research Center
- Polymerase stepsize / Block Lab
Step size of polymerase moving along DNA, as measu ... more - Center for Nanoscale Science and Engineering
The Center for Nanoscale Science and Engineering h ... more