Bio


Syamantak is a postdoctoral researcher in the Pratx Lab at Stanford University. He is involved in developing in-vitro bio-mimetic models of cancer and cancer metastasis for investigating diagnostic and therapeutic agents. Syamantak grew up in a small town in India and had schooling at Ramakrishna Mission Vidyalaya Narendrapur in Kolkata . He completed his Bachelor of Technology (B.Tech), Master of Technology (M.Tech) in Biotechnology and Biochemical Engineering from Indian Institute of Technology, and obtained his PhD in Chemistry from Indian Institute of Technology Mandi. He was trained in molecular biology techniques and drug delivery systems in the lab of Prof. Sudip Ghosh. He worked with Dr. Chayan Nandi to investigate the optical properties of carbon nanodots using ensemble and single molecule spectroscopic techniques. He worked in Joerg Enderlein's group in the University of Goettingen, Germany before joining Stanford.

Honors & Awards


  • Young Investigator Award, AAPM, California Chapter (2020)

Boards, Advisory Committees, Professional Organizations


  • Associate Member, American Association for Cancer Research (AACR) (2019 - Present)
  • Student Member, World Molecular Imaging Society (2020 - Present)

Professional Education


  • Doctor of Philosophy, Indian Institute of Technology, Mandi, Chemistry, Nanoscience (2018)
  • Bachelor of Technology, Indian Institute of Technology, Kharagpur (2012)
  • Master of Technology, Indian Institute of Technology, Kharagpur (2012)

Stanford Advisors


Current Research and Scholarly Interests


My current research interest involves developing in-vitro bio-mimetic models of cancer and cancer metastasis for investigating diagnostic and therapeutic agents.

Lab Affiliations


All Publications


  • High-resolution radioluminescence microscopy of FDG uptake in an engineered 3D tumor-stoma model. European journal of nuclear medicine and molecular imaging Khan, S., Kim, S., Yang, Y. P., Pratx, G. 2021

    Abstract

    PURPOSE: The increased glucose metabolism of cancer cells is the basis for 18F-fluorodeoxyglucose positron emission tomography (FDG-PET). However, due to its coarse image resolution, PET is unable to resolve the metabolic role of cancer-associated stroma, which often influences the metabolic reprogramming of a tumor. This study investigates the use of radioluminescence microscopy for imaging FDG uptake in engineered 3D tumor models with high resolution.METHOD: Multicellular tumor spheroids (A549 lung adenocarcinoma) were co-cultured with GFP-expressing human umbilical vein endothelial cells (HUVECs) within an artificial extracellular matrix to mimic a tumor and its surrounding stroma. The tumor model was constructed as a 200-mum-thin 3D layer over a transparent CdWO4 scintillator plate to allow high-resolution imaging of the cultured cells. After incubation with FDG, the radioluminescence signal was collected by a highly sensitive widefield microscope. Fluorescence microscopy was performed using the same instrument to localize endothelial and tumor cells.RESULTS: Simultaneous and co-localized brightfield, fluorescence, and radioluminescence imaging provided high-resolution information on the distribution of FDG in the engineered tissue. The microvascular stromal compartment as a whole took up a large fraction of the FDG, comparable to the uptake of the tumor spheroids. In vitro gamma counting confirmed that A549 and HUVEC cells were both highly glycolytic with rapid FDG uptake kinetics. Despite the relative thickness of the tissue constructs, an average spatial resolution of 64±4mum was achieved for imaging FDG.CONCLUSION: Our study demonstrates the feasibility of imaging the distribution of FDG uptake in engineered in vitro tumor models. With its high spatial resolution, the method can separately resolve tumor and stromal components. The approach could be extended to more advanced engineered cancer models but also to surgical tissue slices and tumor biopsies.

    View details for DOI 10.1007/s00259-021-05364-6

    View details for PubMedID 33880604

  • Multicellular spheroids as in vitro models of oxygen depletion during FLASH irradiation. International journal of radiation oncology, biology, physics Khan, S., Bassenne, M., Wang, J., Manjappa, R., Melemenidis, S., Breitkreutz, D. Y., Maxim, P. G., Xing, L., Loo, B. W., Pratx, G. 2021

    Abstract

    PURPOSE: The differential response of normal and tumor tissues to ultra-high dose rate radiation (FLASH) has raised new hope for treating solid tumors but, to date, the mechanism remains elusive. One leading hypothesis is that FLASH radiochemically depletes oxygen from irradiated tissues faster than it is replenished through diffusion. The purpose of this study is to investigate these effects within hypoxic multicellular tumor spheroids, through simulations and experiments.MATERIALS AND METHODS: Physicobiological equations were derived to model (i) the diffusion and metabolism of oxygen within spheroids; (ii) its depletion through reactions involving radiation-induced radicals; and (iii) the increase in radioresistance of spheroids, modeled according to the classical oxygen enhancement ratio and linear-quadratic response. These predictions were then tested experimentally in A549 spheroids exposed to electron irradiation at conventional (0.075 Gy/s) or FLASH (90 Gy/s) dose rates. Clonogenic survival, cell viability, and spheroid growth were scored post-radiation. Clonogenic survival of two other cell lines was also investigated.RESULTS: The existence of a hypoxic core in unirradiated tumor spheroids is predicted by simulations and visualized by fluorescence microscopy. Upon FLASH irradiation, this hypoxic core transiently expands, engulfing a large number of well-oxygenated cells. In contrast, oxygen is steadily replenished during slower conventional irradiation. Experimentally, clonogenic survival was around 3-fold higher in FLASH-irradiated spheroid compared to conventional irradiation, but no significant difference was observed for well-oxygenated 2D-cultured cells. This differential survival is consistent with the predictions of the computational model. FLASH irradiation of spheroids resulted in a dose-modifying factor of around 1.3 for doses above 10 Gy.CONCLUSION: Tumor spheroids can be used as a model to study FLASH irradiation in vitro . The improved survival of tumor spheroids receiving FLASH radiation confirms that ultra-fast radiochemical oxygen depletion and its slow replenishment are critical components of the FLASH effect.

    View details for DOI 10.1016/j.ijrobp.2021.01.050

    View details for PubMedID 33545301

  • Lanthanide Metal-Organic Frameworks for Multispectral Radioluminescent Imaging. ACS applied materials & interfaces Neufeld, M. J., Winter, H., Landry, M. R., Goforth, A. M., Khan, S., Pratx, G., Sun, C. 2020

    Abstract

    In this report, we describe the X-ray luminescent properties of two lanthanide-based nanoscale metal-frameworks (nMOFs) and their potential as novel platforms for optical molecular imaging techniques such as X-ray excited radioluminescence (RL) imaging. Upon X-ray irradiation, the nMOFs display sharp tunable emission peaks that span the visible to near-infrared spectral region (400-700 nm) based on the identity of the metal (Eu, Tb, or Eu/Tb). Surface modification of the nMOFs with polyethylene glycol (PEG) resulted in nanoparticles with enhanced aqueous stability that demonstrated both cyto- and hemo-compatibility important prerequisites for biological applications. Importantly, this is the first report to document and investigate the radioluminescent properties of lanthanide nMOFs. Taken together, the observed radioluminescent properties and low in vitro toxicity demonstrated by the nMOFs render them promising candidates for in vivo translation.

    View details for DOI 10.1021/acsami.0c06010

    View details for PubMedID 32442367

  • High-resolution positron emission microscopy of patient-derived tumor organoids. Khan, S., Shin, J., Cheng, N., Kuo, C., Sunwoo, J., Pratx, G. AMER ASSOC CANCER RESEARCH. 2020: 59
  • Tb-Doped core-shell-shell nanophosphors for enhanced X-ray induced luminescence and sensitization of radiodynamic therapy. Biomaterials science Ren, Y. n., Rosch, J. G., Landry, M. R., Winter, H. n., Khan, S. n., Pratx, G. n., Sun, C. n. 2020

    Abstract

    The development of radiation responsive materials, such as nanoscintillators, enables a variety of exciting new theranostic applications. In particular, the ability of nanophosphors to serve as molecular imaging agents in novel modalities, such as X-ray luminescence computed tomography (XLCT), has gained significant interest recently. Here, we present a radioluminescent nanoplatform consisting of Tb-doped nanophosphors with an unique core/shell/shell (CSS) architecture for improved optical emission under X-ray excitation. Owing to the spatial confinement and separation of luminescent activators, these CSS nanophosphors exhibited bright optical luminescence upon irradiation. In addition to standard physiochemical characterization, these CSS nanophosphors were evaluated for their ability to serve as energy mediators in X-ray stimulated photodynamic therapy, also known as radiodynamic therapy (RDT), through attachment of a photosensitizer, rose bengal (RB). Furthermore, cRGD peptide was used as a model targeting agent against U87 MG glioblastoma cells. In vitro RDT efficacy studies suggested the RGD-CSS-RB in combination with X-ray irradiation could induce enhanced DNA damage and increased cell killing, while the nanoparticles alone are well tolerated. These studies support the utility of CSS nanophosphors and warrants their further development for theranostic applications.

    View details for DOI 10.1039/d0bm00897d

    View details for PubMedID 33006335

  • Small molecular organic nanocrystals resemble carbon nanodots in terms of their properties CHEMICAL SCIENCE Khan, S., Sharma, A., Ghoshal, S., Jain, S., Hazra, M. K., Nandi, C. K. 2018; 9 (1): 175–80

    Abstract

    The most commonly observed phenomena in carbon nanodots (CNDs) are the strong excitation wavelength dependent multicolor fluorescence emission and the particle size distribution between 3-5 nm observed using a transmission electron microscope (TEM). However, it is not evident yet whether the emission originates from the particles observed using a TEM. In this article, we show that hydrothermal treatment of citric acid produces methylenesuccinic acid, which gives rise to hydrogen-bonded nano-assemblies with CND-like properties. While single crystal X-ray crystallography confirms the structure of methylenesuccinic acid, fluorescence correlation spectroscopy (FCS) confirms the presence of a molecular fluorophore with an average hydrodynamic diameter of ∼0.9 nm. This size is much smaller than the size of the particles observed using a TEM. We conclude that the particles observed using a TEM are the drying mediated nanocrystals of methylenesuccinic acid.

    View details for PubMedID 29629085

    View details for PubMedCentralID PMC5869300

  • Labelling Proteins with Carbon Nanodots CHEMBIOCHEM Rao, C., Khan, S., Verma, N. C., Nandi, C. 2017; 18 (24): 2385–89

    Abstract

    We present efficient labelling of several proteins with orange-emissive carbon dots. N-Hydroxysuccinimide was used to activate the carboxyl groups of carbon dots, which subsequently reacted with the lysine groups present on the protein. Labelling was confirmed by UV absorption spectroscopy, PAGE and fluorescence correlation spectroscopy. Protein-conjugated carbon dots showed an enhancement in fluorescence lifetime and intensity owing to reduced intramolecular dynamic fluctuations. Single-molecule fluorescence measurements showed reduced fluorescence fluctuations and higher photon budget after protein tagging. Our study opens up opportunities to use carbon dots as highly precise biolabelling probes.

    View details for DOI 10.1002/cbic.201700440

    View details for Web of Science ID 000418111700004

    View details for PubMedID 28985453

  • Charge-Driven Fluorescence Blinking in Carbon Nanodots JOURNAL OF PHYSICAL CHEMISTRY LETTERS Khan, S., Li, W., Karedla, N., Thiart, J., Gregor, I., Chizhik, A. M., Enderlein, J., Nandi, C. K., Chizhik, A. I. 2017; 8 (23): 5751–57

    Abstract

    This study focuses on the mechanism of fluorescence blinking of single carbon nanodots, which is one of their key but less understood properties. The results of our single-particle fluorescence study show that the mechanism of carbon nanodots blinking has remarkable similarities with that of semiconductor quantum dots. In particular, the temporal behavior of carbon nanodot blinking follows a power law both at room and at cryogenic temperatures. Our experimental data suggest that static quenching via Dexter-type electron transfer between surface groups of a nanoparticle plays a major role in the transition of carbon nanodots to off or gray states, whereas the transition back to on states is governed by an electron tunneling from the particle's core. These findings advance our understanding of the complex mechanism of carbon nanodots emission, which is one of the key steps for their application in fluorescence imaging.

    View details for PubMedID 29125299

  • Single-molecule analysis of fluorescent carbon dots towards localization-based super-resolution microscopy METHODS AND APPLICATIONS IN FLUORESCENCE Verma, N. C., Khan, S., Nandi, C. K. 2016; 4 (4): 044006

    Abstract

    The advancement of high-resolution bioimaging has always been dependent on the discovery of bright and easily available fluorescent probes. Fluorescent carbon nanodots, an interesting class of relatively new nanomaterials, have emerged as a versatile alternative due to their superior optical properties, non-toxicity, cell penetrability and easy routes to synthesis. Although a plethora of reports is available on bioimaging using carbon dots, single-molecule-based super-resolution imaging is rare in the literature. In this study, we have systematically characterized the single-molecule fluorescence of three carbon dots and compared them with a standard fluorescent probe. Each of these carbon dots showed a long-lived dark state in the presence of an electron acceptor. The electron transfer mechanism was investigated in single-molecule as well as in ensemble experiments. The average on-off rate between the fluorescent bright and dark states, which is one of the important parameters for single-molecule localization-based super-resolution microscopy, was measured by changing the laser power. We report that the photon budget and on-off rate of these carbon dots were good enough to achieve single-molecule localization with a precision of ~35 nm.

    View details for DOI 10.1088/2050-6120/4/4/044006

    View details for Web of Science ID 000386143800002

    View details for PubMedID 28192299

  • Paper strip based and live cell ultrasensitive lead sensor using carbon dots synthesized from biological media SENSORS AND ACTUATORS B-CHEMICAL Gupta, A., Verma, N., Khan, S., Tiwari, S., Chaudhary, A., Nandi, C. 2016; 232: 107–14
  • Carbon dots for naked eye colorimetric ultrasensitive arsenic and glutathione detection BIOSENSORS & BIOELECTRONICS Gupta, A., Verma, N., Khan, S., Nandi, C. 2016; 81: 465–72

    Abstract

    A novel one-step method for the synthesis of bright, multicolor fluorescent sulphur doped carbon dots (CNDs) has been developed by using simple microwave assisted pyrolysis of citric acid and sodium thiosulphate. The synthesized CNDs showed dual mode naked eye colorimetric ultrasensitive sensing capability both for arsenic [As (III)] and glutathione (GSH) with high selectivity. Using fluorometric assay, the detection limit (DL) for As (III) was found to be as low as 32pM. The selectivity data show that the newly developed CNDs is very specific for As (III) even with interference by high concentrations of other metal ions. The CNDs were also able to detect GSH very selectively over other biothiols like cysteine (Cys) and homo-cysteine (H-cys) with a DL of 43nM, even in blood plasma. The fast kinetic data suggests that the present CNDs assay could be used onsite As (III) detection. The CNDs, further, showed its potential application in high resolution bioimaging of bacterial nucleoid segregation.

    View details for PubMedID 27015150

  • Time-Resolved Emission Reveals Ensemble of Emissive States as the Origin of Multicolor Fluorescence in Carbon Dots NANO LETTERS Khan, S., Gupta, A., Verma, N. C., Nandi, C. K. 2015; 15 (12): 8300–8305

    Abstract

    The origin of photoluminescence in carbon dots has baffled scientists since its discovery. We show that the photoluminescence spectra of carbon dots are inhomogeneously broadened due to the slower relaxation of the solvent molecules around it. This gives rise to excitation-dependent fluorescence that violates the Kasha-Vavilov rule. The time-resolved experiment shows significant energy redistribution, relaxation among the emitting states, and spectral migration of fluorescence spectra in the nanosecond time scale. The excitation-dependent multicolor emission in time-integrated spectra is typically governed by the relative population of these emitting states.

    View details for PubMedID 26566016

  • Kinetics of protein adsorption on gold nanoparticle with variable protein structure and nanoparticle size JOURNAL OF CHEMICAL PHYSICS Khan, S., Gupta, A., Verma, N. C., Nandi, C. K. 2015; 143 (16): 164709

    Abstract

    The spontaneous protein adsorption on nanomaterial surfaces and the formation of a protein corona around nanoparticles are poorly understood physical phenomena, with high biological relevance. The complexity arises mainly due to the poor knowledge of the structural orientation of the adsorbed proteins onto the nanoparticle surface and difficulties in correlating the protein nanoparticle interaction to the protein corona in real time scale. Here, we provide quantitative insights into the kinetics, number, and binding orientation of a few common blood proteins when they interact with citrate and cetyltriethylammoniumbromide stabilized spherical gold nanoparticles with variable sizes. The kinetics of the protein adsorption was studied experimentally by monitoring the change in hydrodynamic diameter and zeta potential of the nanoparticle-protein complex. To understand the competitive binding of human serum albumin and hemoglobin, time dependent fluorescence quenching was studied using dual fluorophore tags. We have performed molecular docking of three different proteins--human serum albumin, bovine serum albumin, and hemoglobin--on different nanoparticle surfaces to elucidate the possible structural orientation of the adsorbed protein. Our data show that the growth kinetics of a protein corona is exclusively dependent on both protein structure and surface chemistry of the nanoparticles. The study quantitatively suggests that a general physical law of protein adsorption is unlikely to exist as the interaction is unique and specific for a given pair.

    View details for DOI 10.1063/1.4934605

    View details for Web of Science ID 000364235800054

    View details for PubMedID 26520545

  • Reversible Photoswitching of Carbon Dots SCIENTIFIC REPORTS Khan, S., Verma, N., Gupta, A., Nandi, C. 2015; 5: 11423

    Abstract

    We present a method of reversible photoswitching in carbon nanodots with red emission. A mechanism of electron transfer is proposed. The cationic dark state, formed by the exposure of red light, is revived back to the bright state with the very short exposure of blue light. Additionally, the natural on-off state of carbon dot fluorescence was tuned using an electron acceptor molecule. Our observation can make the carbon dots as an excellent candidate for the super-resolution imaging of nanoscale biomolecules within the cell.

    View details for PubMedID 26078266

  • Nitrogen-doped, thiol-functionalized carbon dots for ultrasensitive Hg(II) detection CHEMICAL COMMUNICATIONS Gupta, A., Chaudhary, A., Mehta, P., Dwivedi, C., Khan, S., Verma, N., Nandi, C. 2015; 51 (53): 10750–53

    Abstract

    Nitrogen-doped, PEGylated carbon dots (C-dots) have been synthesized for the detection of mercury ions (Hg(2+)). The detection limit was found to be 6.8 nM. However, upon functionalization with dithiothreitol (DTT), it reached to as low as 18 pM. The C-dots-Hg(2+) system was also able to efficiently detect biothiols.

    View details for DOI 10.1039/c5cc03019f

    View details for Web of Science ID 000356453200039

    View details for PubMedID 26051389

  • Orientational switching of protein conformation as a function of nanoparticle curvature and their geometrical fitting JOURNAL OF CHEMICAL PHYSICS Khan, S., Gupta, A., Chaudhary, A., Nandi, C. K. 2014; 141 (8): 084707

    Abstract

    Among the various surface properties, nanoparticle curvature has a direct effect on the inner root of protein nanoparticle interaction. However, the orientation of adsorbed proteins onto the nanoparticle surface and its binding mechanism still remains elusive because of the lack of in-depth knowledge at the molecular level. Here, we demonstrate detail molecular insights of the orientational switching of several serum proteins as a function of nanoparticle curvature using theoretical simulation along with some experimental results. With the variation of binding stability, four distinctly different classes of orientation were observed for human serum albumin, whereas only two unique classes of conformations were observed for ubiquitin, insulin, and haemoglobin. As a general observation, our data suggested that orientations were exclusively dependent on the specific protein structure and the geometrical fitting onto the nanoparticle surface.

    View details for PubMedID 25173030

  • Morphological effect of gold nanoparticles on the adsorption of bovine serum albumin PHYSICAL CHEMISTRY CHEMICAL PHYSICS Chaudhary, A., Gupta, A., Khan, S., Nandi, C. 2014; 16 (38): 20471–82

    Abstract

    Various properties of gold nanoparticles (GNPs) are found to play crucial roles in their biological activity. Among them, the morphology and surface chemistry are extremely important. This is because of differences in surface energies of various crystal facets arising from a large fraction of edges, corners and vertices. In the present work, we provide a comparative study on the adsorption and binding affinities of bovine serum albumin (BSA) onto triangular gold nanoplates (TGNP) and gold nanorods (GNR). The results were compared with similar size of both CTAB and citrate stabilized spherical GNPs. Our data suggested stronger binding of BSA on citrate stabilized spherical GNPs whereas TGNP shows the weakest binding among all the GNPs. A blue shift of approximately 20 nm in tryptophan fluorescence was observed for all CTAB stabilized GNPs, indicating the local dielectric changes surrounding the tryptophan residue. Loss of the secondary structure was also observed for all CTAB stabilized GNPs. No spectral shift was observed for citrate stabilized spherical GNPs though maximum quenching of fluorescence and minimum structural loss was observed. With the help of molecular simulation recently developed by our group, a binding model is proposed to explain all the above experimental results.

    View details for PubMedID 25140357

  • Controlling the Fate of Protein Corona by Tuning Surface Properties of Nanoparticles JOURNAL OF PHYSICAL CHEMISTRY LETTERS Khan, S., Gupta, A., Nandi, C. 2013; 4 (21): 3747–52

    View details for DOI 10.1021/jz401874u

    View details for Web of Science ID 000326845200046