Raman Ganti

Bio: Raman Ganti is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Pressure gradient & Cauchy stress tensor. The author has an hindex of 9, co-authored 15 publications receiving 207 citations. Previous affiliations of Raman Ganti include University of Pennsylvania & University of Cambridge.

Molecular Simulation of Thermo-osmotic Slip.

Abstract: Thermo-osmotic slip-the flow induced by a thermal gradient along a surface-is a well-known phenomenon, but curiously there is a lack of robust molecular-simulation techniques to predict its magnitude. Here, we compare three different molecular-simulation techniques to compute the thermo-osmotic slip at a simple solid-fluid interface. Although we do not expect the different approaches to be in perfect agreement, we find that the differences are barely significant for a range of different physical conditions, suggesting that practical molecular simulations of thermo-osmotic slip are feasible.

Diffraction phase microscopy: monitoring nanoscale dynamics in materials science [Invited]

Abstract: Quantitative phase imaging (QPI) utilizes the fact that the phase of an imaging field is much more sensitive than its amplitude. As fields from the source interact with the specimen, local variations in the phase front are produced, which provide structural information about the sample and can be used to reconstruct its topography with nanometer accuracy. QPI techniques do not require staining or coating of the specimen and are therefore nondestructive. Diffraction phase microscopy (DPM) combines many of the best attributes of current QPI methods; its compact configuration uses a common-path off-axis geometry which realizes the benefits of both low noise and single-shot imaging. This unique collection of features enables the DPM system to monitor, at the nanoscale, a wide variety of phenomena in their natural environments. Over the past decade, QPI techniques have become ubiquitous in biological studies and a recent effort has been made to extend QPI to materials science applications. We briefly review several recent studies which include real-time monitoring of wet etching, photochemical etching, surface wetting and evaporation, dissolution of biodegradable electronic materials, and the expansion and deformation of thin-films. We also discuss recent advances in semiconductor wafer defect detection using QPI.

How the T cell signaling network processes information to discriminate between self and agonist ligands.

Abstract: T cells exhibit remarkable sensitivity and selectivity in detecting and responding to agonist peptides (p) bound to MHC molecules in a sea of self pMHC molecules. Despite much work, understanding of the underlying mechanisms of distinguishing such ligands remains incomplete. Here, we quantify T cell discriminatory capacity using channel capacity, a direct measure of the signaling network's ability to discriminate between antigen-presenting cells (APCs) displaying either self ligands or a mixture of self and agonist ligands. This metric shows how differences in information content between these two types of peptidomes are decoded by the topology and rates of kinetic proofreading signaling steps inside T cells. Using channel capacity, we constructed numerically substantiated hypotheses to explain the discriminatory role of a recently identified slow LAT Y132 phosphorylation step. Our results revealed that in addition to the number and kinetics of sequential signaling steps, a key determinant of discriminatory capability is spatial localization of a minimum number of these steps to the engaged TCR. Biochemical and imaging experiments support these findings. Our results also reveal the discriminatory role of early negative feedback and necessary amplification conferred by late positive feedback.

Hamiltonian Transformation to Compute Thermo-osmotic Forces.

Abstract: If a thermal gradient is applied along a fluid-solid interface, the fluid experiences a thermo-osmotic force. In the steady state, this force is balanced by the gradient of the shear stress. Surprisingly, there appears to be no unique microscopic expression that can be used for computing the magnitude of the thermo-osmotic force. Here we report how, by treating the mass $M$ of the fluid particles as a tensor in the Hamiltonian, we can eliminate the balancing shear force in a nonequilibrium simulation and therefore compute the thermo-osmotic force at simple solid-fluid interfaces. We compare the nonequilibrium force measurement with estimates of the thermo-osmotic force based on computing gradients of the stress tensor. We find that the thermo-osmotic force as measured in our simulations cannot be derived from the most common microscopic definitions of the stress tensor.

Measuring the Nonuniform Evaporation Dynamics of Sprayed Sessile Microdroplets with Quantitative Phase Imaging.

Abstract: We demonstrate real-time quantitative phase imaging as a new optical approach for measuring the evaporation dynamics of sessile microdroplets. Quantitative phase images of various droplets were captured during evaporation. The images enabled us to generate time-resolved three-dimensional topographic profiles of droplet shape with nanometer accuracy and, without any assumptions about droplet geometry, to directly measure important physical parameters that characterize surface wetting processes. Specifically, the time-dependent variation of the droplet height, volume, contact radius, contact angle distribution along the droplet's perimeter, and mass flux density for two different surface preparations are reported. The studies clearly demonstrate three phases of evaporation reported previously: pinned, depinned, and drying modes; the studies also reveal instances of partial pinning. Finally, the apparatus is employed to investigate the cooperative evaporation of the sprayed droplets. We observe and explain the neighbor-induced reduction in evaporation rate, that is, as compared to predictions for isolated droplets. In the future, the new experimental methods should stimulate the exploration of colloidal particle dynamics on the gas-liquid-solid interface.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Spatial light interference microscopy (SLIM)

Abstract: We present SLIM, a new optical method measuring optical pathlength changes of 0.3 nm spatially and 0.03nm temporally. SLIM combines two classic ideas in light imaging: Zernike’s phase contrast microscopyand Gabor’s holography.

HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies

Abstract: Summary Broadly neutralizing antibodies (bnAbs) against the N332 supersite of the HIV envelope (Env) trimer are the most common bnAbs induced during infection, making them promising leads for vaccine design. Wild-type Env glycoproteins lack detectable affinity for supersite-bnAb germline precursors and are therefore unsuitable immunogens to prime supersite-bnAb responses. We employed mammalian cell surface display to design stabilized Env trimers with affinity for germline-reverted precursors of PGT121-class supersite bnAbs. The trimers maintained native-like antigenicity and structure, activated PGT121 inferred-germline B cells ex vivo when multimerized on liposomes, and primed PGT121-like responses in PGT121 inferred-germline knockin mice. Design intermediates have levels of epitope modification between wild-type and germline-targeting trimers; their mutation gradient suggests sequential immunization to induce bnAbs, in which the germline-targeting prime is followed by progressively less-mutated design intermediates and, lastly, with native trimers. The vaccine design strategies described could be utilized to target other epitopes on HIV or other pathogens.

Osmosis, from molecular insights to large-scale applications.

Abstract: Osmosis is a universal phenomenon occurring in a broad variety of processes and fields. It is the archetype of entropic forces, both trivial in its fundamental expression - the van 't Hoff perfect gas law - and highly subtle in its physical roots. While osmosis is intimately linked with transport across membranes, it also manifests itself as an interfacial transport phenomenon: the so-called diffusio-osmosis and -phoresis, whose consequences are presently actively explored for example for the manipulation of colloidal suspensions or the development of active colloidal swimmers. Here we give a global and unifying view of the phenomenon of osmosis and its consequences with a multi-disciplinary perspective. Pushing the fundamental understanding of osmosis allows one to propose new perspectives for different fields and we highlight a number of examples along these lines, for example introducing the concepts of osmotic diodes, active separation and far from equilibrium osmosis, raising in turn fundamental questions in the thermodynamics of separation. The applications of osmosis are also obviously considerable and span very diverse fields. Here we discuss a selection of phenomena and applications where osmosis shows great promises: osmotic phenomena in membrane science (with recent developments in separation, desalination, reverse osmosis for water purification thanks in particular to the emergence of new nanomaterials); applications in biology and health (in particular discussing the kidney filtration process); osmosis and energy harvesting (in particular, osmotic power and blue energy as well as capacitive mixing); applications in detergency and cleaning, as well as for oil recovery in porous media.

Modulation of Molecular Spatial Distribution and Chemisorption with Perforated Nanosheets for Ethanol Electro-oxidation.

Abstract: Integrating thermodynamically favorable ethanol reforming reactions with hybrid water electrolysis will allow room-temperature production of high-value organic products and decoupled hydrogen evolution. However, electrochemical reforming of ethanol has not received adequate attention due to its low catalytic efficiency and poor selectivity, which are caused by the multiple groups and chemical bonds of ethanol. In addition to the thermodynamic properties affected by the electronic structure of the catalyst, the dynamics of molecule/ion dynamics in electrolytes also play a significant role in the efficiency of a catalyst. The relatively large size and viscosity of the ethanol molecule necessitates large channels for molecule/ion transport through catalysts. Perforated CoNi hydroxide nanosheets are proposed as a model catalyst to synergistically regulate the dynamics of molecules and electronic structures. Molecular dynamics simulations directly reveal that these nanosheets can act as a "dam" to enrich ethanol molecules and facilitate permeation through the nanopores. Additionally, the charge transfer behavior of heteroatoms modifies the local charge density to promote molecular chemisorption. As expected, the perforated nanosheets exhibit a small potential (1.39 V) and high Faradaic efficiency for the conversion of ethanol into acetic acid. Moreover, the concept in this work provides new perspectives for exploring other molecular catalysts.