School of Humanities and Sciences
Showing 201-250 of 304 Results
-
Suman Patra
Postdoctoral Scholar, Chemistry
BioDr. Suman Patra is a postdoctoral researcher in the Department of Chemistry at Stanford University, working under the mentorship of Prof. Edward I. Solomon. His research focuses on uncovering the mechanistic intricacies of non-coupled binuclear copper (NBC) enzymes, particularly tyramine β-monooxygenase (TBM), which catalyzes oxygen activation and selective C–H bond hydroxylation.His work integrates high-resolution spectroscopy, transient kinetics, and protein biochemistry to probe the formation, structure, and reactivity of short-lived copper-oxygen intermediates. As part of this effort, he performs cell culture and protein purification, enabling the isolation of active, recombinant copper enzymes for detailed spectroscopic and mechanistic studies. Through a multi-spectroscopic approach, primarily UV-Vis, CD, MCD, EXAFS, EPR, resonance Raman, and stopped-flow absorption spectroscopy, he investigates how the geometric and electronic structure of the active sites modulate reactivity and enable O₂ activation without direct Cu–Cu coupling.
Dr. Patra earned his Ph.D. in Chemistry from the Indian Association for the Cultivation of Science (IACS), Kolkata, under the supervision of Prof. Abhishek Dey, where he developed iron porphyrin-based electrocatalysts for the selective reduction of CO₂. His research emphasized mechanistic analysis using electrochemical methods coupled with in situ spectro-electrochemistry to monitor redox transitions and catalytic intermediates under applied potentials. These studies were complemented by density functional theory (DFT) calculations, which he used to model key intermediates, protonation pathways, and redox energetics, thereby providing molecular-level insight into how second-sphere interactions and ligand environments influence catalytic behaviour. His integrative experimental–computational approach provided a detailed understanding of structure-function relationships in multi-electron CO₂ reduction.
The mechanistic perspective and technical skillset developed during his doctoral work, particularly in combining spectroscopy, electrochemistry, and computation, now form the foundation of his postdoctoral research. His current studies extend those same principles to more complex metalloenzyme systems, addressing similar core questions about the role of electronic structure, metal-ligand coordination, and local environment in controlling reactivity. His long-term goal is to bridge synthetic and biological catalysis through a mechanistic lens, contributing to the development of efficient, selective systems for small-molecule activation and sustainable energy transformations.
Dr. Patra received his M.Sc. in Chemistry from the Indian Institute of Technology (IIT) Guwahati after qualifying the national IIT-JAM examination and completed his B.Sc. in Chemistry at St. Xavier’s College, Kolkata. Over the course of his academic training, he has cultivated a multidisciplinary research identity that spans coordination chemistry, spectroscopy, electrochemical catalysis, and theoretical modelling. His scientific vision centres on using spectroscopic and computational insight to guide the rational design of catalysts for environmentally relevant redox chemistry. -
Robert Pecora
Professor of Chemistry, Emeritus
Current Research and Scholarly InterestsThe development of the basic principles behind the dynamic light scattering (DLS) technique and its application to a wide variety of liquid systems is one of Pecora's outstanding contributions to physical chemistry. DLS is now an indispensable tool in the repertoire of polymer, colloid and biophysical chemists. It is generally accepted to be one of the best methods for measuring the mutual diffusion coefficients and, in dilute systems, the hydrodynamic sizes of polymers and particulates in solution or suspension. It is widely used, among other things, for studying size distributions of polymer and colloid dispersions; for testing theories of polymer dynamics in dilute and concentrated systems; and for studying interactions between macromolecules and colloidal particles in liquid dispersions. The basic work that established the foundation of this technique was done in the 1960s. Pecora has revisited this area over the years-formulating theories, for instance, of scattering from hollow spheres, large cylindrically symmetric molecules and wormlike chains.
An experimental program began in the early seventies resulted in a now classic series of studies on the rotational dynamics of small molecules in liquids. This work, utilizing mainly depolarized DLS and carbon 13 nuclear magnetic relaxation, has had a wide impact in the area of liquid state dynamics.
It was also during this period that the theoretical foundation for the fluorescence correlation spectroscopy technique (FCS) was formulated. Because of recent advances in equipment and materials, this technique has recently been revived and is now a powerful tool in biophysics.
The experimental and theoretical techniques developed for the study of the dynamics of relatively simple small molecule liquids have been used to investigate more complex systems such as the rotation of small molecule solvents in glassy and amorphous polymers. The resonance- enhanced depolarized light scattering technique was also developed in this period.
Extensive studies using depolarized dynamic light scattering (using the Fabry-Perot interferometer) as well as photon correlation spectroscopy, NMR, FCS and small angle X-ray scattering to the dynamics of oligonucleotides have determined the hydrodynamic diameter of DNA and the internal bending angles of the bases. They also provided support for relations relating hydrodynamic parameters to molecular dimensions for short rodlike molecules and “polyelectrolyte effects” on the translational and rotational motions of these highly charged molecules.
A major area of experimental and theoretical study has been the study of the dynamics of rigid and semirigid rodlike polymers in both dilute and semidilute dispersions. The work on translation and rotation of poly (-benzyl-L-glutamate) in semidilute solution is a foremost early work in this area.
The Pecora group has synthesized and studied the dynamics of model
rigid rod/sphere composite liquids. Studies of the translation of dilute spheres through solutions of the rods as functions of the rod and sphere sizes and the rod concentrations have provided the stimulus for more experiment and theoretical work in this area. Transient electric birefringence decay studies of the rotation of dilute rigid rod polymers in suspensions of comparably sized spherical particles have revealed scaling laws for the rod rotation.
A unique feature of part of this work on rigid and semirigid rodlike polymers is the utilization of genetic engineering techniques to construct a monodisperse, homologous series of DNA restriction fragments. These biologically-produced fragments have served as well-characterized model macromolecules for solution studies of the dynamics of semirigid rodlike polymers.
The well-regarded book of Pecora and Berne on dynamic light scattering, first published in 1976, has become a major reference work. It is now a Dover paperback. -
Krishna Raghavan
Ph.D. Student in Chemistry, admitted Autumn 2024
BioKrishna is originally from the Detroit area of Michigan, and completed his undergraduate studies in biological chemistry and chemistry at the University of Chicago. He is currently a second-year PhD student concentrating in biophysical chemistry, in the lab of Prof. Bianxiao Cui.
-
Alok Ranjan
Physical Science Research Scientist
BioAccomplished Research Scientist with a rich history (6-8 years) of spearheading cutting-edge research projects. Proficient in synthesizing and analyzing new compounds with therapeutic potential. Experienced in utilizing both structure and property-based strategies to identify promising drug candidates. Led multidisciplinary teams to innovate solutions, enhanced drug discovery efficiency by integrating advanced computational techniques. Committed to continuous learning and staying well-informed of the latest trends in medicinal chemistry and drug design.
-
Jianghong Rao
Professor of Radiology (Molecular Imaging Program at Stanford) and, by courtesy, of Chemistry
Current Research and Scholarly InterestsProbe chemistry and nanotechnology for molecular imaging and diagnostics
-
Grant M. Rotskoff
Assistant Professor of Chemistry
BioGrant Rotskoff studies the nonequilibrium dynamics of living matter with a particular focus on self-organization from the molecular to the cellular scale. His work involves developing theoretical and computational tools that can probe and predict the properties of physical systems driven away from equilibrium. Recently, he has focused on characterizing and designing physically accurate machine learning techniques for biophysical modeling. Prior to his current position, Grant was a James S. McDonnell Fellow working at the Courant Institute of Mathematical Sciences at New York University. He completed his Ph.D. at the University of California, Berkeley in the Biophysics graduate group supported by an NSF Graduate Research Fellowship. His thesis, which was advised by Phillip Geissler and Gavin Crooks, developed theoretical tools for understanding nonequilibrium control of the small, fluctuating systems, such as those encountered in molecular biophysics. He also worked on coarsegrained models of the hydrophobic effect and self-assembly. Grant received an S.B. in Mathematics from the University of Chicago, where he became interested in biophysics as an undergraduate while working on free energy methods for large-scale molecular dynamics simulations.
Research Summary
My research focuses on theoretical and computational approaches to "mesoscale" biophysics. Many of the cellular phenomena that we consider the hallmarks of living systems occur at the scale of hundreds or thousands of proteins. Processes like the self-assembly of organelle-sized structures, the dynamics of cell division, and the transduction of signals from the environment to the machinery of the cell are not macroscopic phenomena—they are the result of a fluctuating, nonequilibrium dynamics. Experimentally probing mesoscale systems remains extremely difficult, though it is continuing to benefit from advances in cryo-electron microscopy and super-resolution imaging, among many other techniques. Predictive and explanatory models that resolve the essential physics at these intermediate scales have the power to both aid and enrich the understanding we are presently deriving from these experimental developments.
Major parts of my research include:
1. Dynamics of mesoscale biophysical assembly and response.— Biophysical processes involve chemical gradients and time-dependent external signals. These inherently nonequilibrium stimuli drive supermolecular organization within the cell. We develop models of active assembly processes and protein-membrane interactions as a foundation for the broad goal of characterizing the properties of nonequilibrium biomaterials.
2. Machine learning and dimensionality reduction for physical models.— Machine learning techniques are rapidly becoming a central statistical tool in all domains of scientific research. We apply machine learning techniques to sampling problems that arise in computational chemistry and develop approaches for systematically coarse-graining physical models. Recently, we have also been exploring reinforcement learning in the context of nonequilibrium control problems.
3. Methods for nonequilibrium simulation, optimization, and control.— We lack well-established theoretical frameworks for describing nonequilibrium states, even seemingly simple situations in which there are chemical or thermal gradients. Additionally, there are limited tools for predicting the response of nonequilibrium systems to external perturbations, even when the perturbations are small. Both of these problems pose key technical challenges for a theory of active biomaterials. We work on optimal control, nonequilibrium statistical mechanics, and simulation methodology, with a particular interest in developing techniques for importance sampling configurations from nonequilibrium ensembles. -
Silvia Russi
Research and Development Scientist and Engineer, Stanford Synchrotron Radiation Lightsource Laboratory (SSRL)
Current Role at StanfordBeamline Scientist, Structural Molecular Biology (SMB), Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Stanford University
-
Jennifer Schwartz Poehlmann
Senior Lecturer of Chemistry
BioReaching out to Stanford’s diverse body of students and beyond to share the excitement of scientific discovery has been a growing passion for Dr. Jennifer Schwartz Poehlmann. In addition to coordinating and co-teaching Stanford’s freshmen chemistry sequence, she takes a leadership role in developing training programs for teaching assistants and enhancing classroom and lab experiences for undergraduates, while also providing STEM learning opportunities for incoming freshmen and local high school students.
Jennifer Schwartz Poehlmann studied chemistry at Washington University in Saint Louis Missouri (A.B. 2002) before coming to Stanford University as a graduate student (Ph.D. 2008). Her thesis work under Prof. Edward Solomon addressed structural contributions to reactivity in active sites of non-heme di-iron enzymes, including ferritins. She joined the Stanford Center (now Vice Provost) for Teaching and Learning as a Teaching Fellow in 2008. In 2009, she became Lecturer and Introductory Course Coordinator for the Department of Chemistry, and in 2011 was promoted to Senior Lecturer. She has received multiple awards for her teaching and training work, including the Walter J. Gores Award for Excellence in Teaching, Dean’s Award for Achievements in Teaching, Hoagland Award Fund for Innovations in Undergraduate Teaching, and Society of Latino Engineers and School of Engineering’s Professor of the Year Award.
Teaching
Dr. Schwartz coordinates and co-teaches the introductory course sequence of Chem31A, 31B, and 33 for about 450 students each year. She has also created a set of companion courses (Chem31A-C, 31B-C, and 33-C) designed to provide motivated students an opportunity to build stronger study habits and problem solving tools that help them persevere in the sciences regardless of prior science background. In parallel, she has been involved in the creation and teaching of the Leland Scholars Program, which facilitates the transition to college for incoming freshman intending to study in STEM or pre-health fields.
Instructor Training
Dr. Schwartz has always believed that well-prepared and enthusiastic teachers inspire and motivate learning, yet excellent teaching requires training, feedback, reflection and support. She has worked both within the department and more broadly to help ensure that teaching assistants throughout the university receive the training, practice and mentorship they need to grow and excel as educators. She previously directed the Department of Chemistry’s TA Training program and, with the Vice Provost for Teaching and Learning, co-founded and directs the Mentors in Teaching Program, MinT, which provides training and resources to teaching mentors from more than 15 departments on campus. Through MinT, advanced graduate students learn effective ways to mentor TAs, through mid-quarter feedback, classroom observation, establishment of teaching goals, and workshops that enable new TAs to better engage with students in the classroom.
Enhanced Learning Experiences
Dr. Schwartz has been heavily involved in the development of hands-on, guided-inquiry lab activities that are now fully integrated into lab/lecture courses throughout the introductory general and organic chemistry sequence. Through the “Inspiring Future Scientists in Chemistry” Outreach Program, she is also helping to bring the excitement of exploring real-world chemistry into local high schools. She works with local high school teachers to design lab experiences that reinforce and compliment the chemistry concepts in the California State curriculum. Stanford Chemistry students take these activities to local high schools, providing hundreds of students the opportunity to work with enthusiastic young scientists while getting hands-on experience in chemistry. The program aims to demonstrate how chemistry relates to the ‘real world’ and to promote an appreciation for both science and higher education. -
Fangfang Shen
Physical Science Research Scientist
Current Research and Scholarly InterestsIdentify protein inhibitors and develop novel specific protein delivery systems.
-
Edward I. Solomon
Monroe E. Spaght Professor of Chemistry, Emeritus
Current Research and Scholarly InterestsProf. Solomon's work spans physical-inorganic, bioinorganic, and theoretical-inorganic chemistry, focusing on spectroscopic elucidation of the electronic structure of transition metal complexes and its contribution to reactivity. He has advanced our understanding of metal sites involved in electron transfer, copper sites involved in O2 binding, activation and reduction to water, structure/function correlations over non-heme iron enzymes, and correlation of biological to heterogeneous catalysis.
-
Daniel Stack
Associate Professor of Chemistry
BioResearch in the Stack group focuses on the mechanism of dioxygen activation and the subsequent oxidative reactivity with primarily copper complexes ligated by imidazoles or histamines. Specifically, the group is interested in substrate hydroxylations and full dioxygen reduction. The remarkable specificity and energy efficiency of metalloenzymes provide the inspiration for the work. Trapping and characterizing immediate species, primarily at low temperatures, provide key mechanistic insights especially through substrate reactivity along with spectroscopic and metrical correlation to DFT calculations. Our objective is to move these efficient enzymatic mechanisms into small synthetic complexes, not only to reproduce biological reactivity, but more importantly to move the oxidative mechanism beyond that possible in the protein matrix.
Daniel Stack was born, raised and attended college in Portland Oregon. He received his B.A. from Reed College in 1982 (Phi Beta Kappa), working with Professor Tom Dunne on weak nickel-pyrazine complexes. In Boston, he pursued his doctoral study in synthetic inorganic chemistry at Harvard University (Ph.D., 1988) with Professor R. H. Holm, investigating site-differentiated synthetic analogues of biological Fe4S4 cubanes. As an NSF Postdoctoral Fellow with Professor K. N. Raymond at the University of California at Berkeley, he worked on synthesizing new, higher iron affinity ligands similar to enterobactin, a bacterial iron sequestering agent. He started his independent career in 1991 at Stanford University primarily working on oxidation catalysis and dioxygen activation, and was promoted to an Associate Professor in 1998. His contributions to undergraduate education have been recognized at the University level on several occasions, including the Dinkelspiel Award for Outstanding Contribution to Undergraduate Education in 2003.
Areas of current focus include:
Copper Dioxygen Chemistry
Our current interests focus on stabilizing species formed in the reaction of dioxygen with Cu(I) complexes formed with biologically relevant imidazole or histamine ligation. Many multi-copper enzymes ligated in this manner are capable of impressive hydroxylation reactions, including oxidative depolymerization of cellulose, methane oxidation, and energy-efficient reduction of dioxygen to water. Oxygenation of such complexes at extreme solution temperatures (-125°C) yield transient Cu(III) containing complexes. As Cu(III) is currently uncharacterized in any biological enzyme, developing connections between the synthetic and biological realms is a major focus.
