output
19992025
most citedInduced fit, conformational selection and independent dynamic segments: an extended view of binding events

839 citations

25 papers

physics.ao-ph2025★ 3 cited

Advancing global sea ice prediction capabilities using a fully-coupled climate model with integrated machine learning

William Gregory, Mitchell Bushuk, Yong-Fei Zhang +4

We showcase a hybrid modeling framework which embeds machine learning (ML) inference into the GFDL SPEAR climate model, for online sea ice bias correction during a set of global fu…

q-fin.MF2024

Backtesting Framework for Concentrated Liquidity Market Makers on Uniswap V3 Decentralized Exchange

Andrey Urusov, Rostislav Berezovskiy, Yury Yanovich

Decentralized finance (DeFi) has revolutionized the financial landscape, with protocols like Uniswap offering innovative automated market-making mechanisms. This article explores t…

quant-ph2023★ 10 cited

The quantum detection of projectors in finite-dimensional algebras and holography

Joseph Ben Geloun, Sanjaye Ramgoolam

We define the computational task of detecting projectors in finite dimensional associative algebras with a combinatorial basis, labelled by representation theory data, using combin…

astro-ph.IM2023★ 122 cited

The James Webb Space Telescope Mission: Optical Telescope Element Design, Development, and Performance

Michael W. McElwain, Lee D. Feinberg, Marshall D. Perrin +126

The James Webb Space Telescope (JWST) is a large, infrared space telescope that has recently started its science program which will enable breakthroughs in astrophysics and planeta…

physics.flu-dyn2014★ 4 cited

The Numerical Simulation of Ship Waves using Cartesian Grid Methods

Mark Sussman, Douglas G. Dommermuth

Two different cartesian-grid methods are used to simulate the flow around the DDG 5415. The first technique uses a "coupled level-set and volume-of-fluid" (CLS) technique to model…

physics.ao-ph2013★ 6 cited

Wave-wave interactions and deep ocean acoustics

Zachary Guralnik, William Farrell, John Bourdelais +1

Deep ocean acoustics, in the absence of shipping and wildlife, is driven by surface processes. Best understood is the signal generated by non-linear surface wave interactions, the…

cs.AI2013

Robust Planning in Uncertain Environments

Stephen G. Pimentel, Lawrence M. Brem

This paper describes a novel approach to planning which takes advantage of decision theory to greatly improve robustness in an uncertain environment. We present an algorithm which…

physics.plasm-ph2012★ 13 cited

Observed transition from Richtmyer-Meshkov jet formation through feedout oscillations to Rayleigh-Taylor instability in a laser target

Y. Aglitskiy, M. Karasik, A. L. Velikovich +8

Experimental study of hydrodynamic perturbation evolution triggered by a laser-driven shock wave breakout at the free rippled rear surface of a plastic target is reported. At sub-m…

cond-mat.mtrl-sci2012★ 41 cited

Electrical injection and detection of spin accumulation in Ge at room temperature

A. T. Hanbicki, S. -. F. Cheng, R. Goswami +2

We inject spin-polarized electrons from an Fe/MgO tunnel barrier contact into n-type Ge(001) substrates with electron densities 2e16 < n < 8e17 cm-3, and electrically detect the re…

q-bio.MN2011★ 151 cited

Allo-network drugs: harnessing allostery in cellular networks

Ruth Nussinov, Chung-Jung Tsai, Peter Csermely

Allosteric drugs are increasingly used because they produce fewer side effects. Allosteric signal propagation does not stop at the 'end' of a protein, but may be dynamically transm…

physics.acc-ph2010★ 1 cited

Validation of frequency and mode extraction calculations from time-domain simulations of accelerator cavities

T. M. Austin, J. R. Cary, S. Ovtchinnikov +2

The recently developed frequency extraction algorithm [G.R. Werner and J.R. Cary, J. Comp. Phys. 227, 5200 (2008)] that enables a simple FDTD algorithm to be transformed into an ef…

q-bio.BM2010★ 839 cited

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

Peter Csermely, Robin Palotai, Ruth Nussinov

Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which…

quant-ph2009★ 65 cited

Could light harvesting complexes exhibit non-classical effects at room temperature?

Mark M. Wilde, James M. McCracken, Ari Mizel

Mounting experimental and theoretical evidence suggests that coherent quantum effects play a role in the efficient transfer of an excitation from a chlorosome antenna to a reaction…

quant-ph2009★ 8 cited

Entanglement generation with a quantum channel and a shared state

Mark M. Wilde, Min-Hsiu Hsieh

We introduce a new protocol, the channel-state coding protocol, to quantum Shannon theory. This protocol generates entanglement between a sender and receiver by coding for a noisy…

quant-ph2009★ 41 cited

On the logical operators of quantum codes

Mark M. Wilde

I show how applying a symplectic Gram-Schmidt orthogonalization to the normalizer of a quantum code gives a different way of determining the code's logical operators. This approach…

quant-ph2009★ 27 cited

Quantum Shift Register Circuits

Mark M. Wilde

A quantum shift register circuit acts on a set of input qubits and memory qubits, outputs a set of output qubits and updated memory qubits, and feeds the memory back into the devic…

quant-ph2009★ 21 cited

Public and private communication with a quantum channel and a secret key

Min-Hsiu Hsieh, Mark M. Wilde

We consider using a secret key and a noisy quantum channel to generate noiseless public communication and noiseless private communication. The optimal protocol for this setting is…

quant-ph2008★ 30 cited

Critically damped quantum search

Ari Mizel

Although measurement and unitary processes can accomplish any quantum evolution in principle, thinking in terms of dissipation and damping can be powerful. We propose a modificatio…

physics.comp-ph2008★ 382 cited

The RAGE radiation-hydrodynamic code

Michael Gittings, Robert Weaver, Michael Clover +9

We describe RAGE, the ``Radiation Adaptive Grid Eulerian'' radiation-hydrodynamics code, including its data structures, its parallelization strategy and performance, its hydrodynam…

astro-ph2007★ 61 cited

May 12 1997 Cme Event: I. a Simplified Model of the Pre-Eruptive Magnetic Structure

V. S. Titov, Z. Mikic, J. A. Linker +1

A simple model of the coronal magnetic field prior to the CME eruption on May 12 1997 is developed. First, the magnetic field is constructed by superimposing a large-scale backgrou…

astro-ph2007★ 91 cited

Structure and Dynamics of the Sun's Open Magnetic Field

S. K. Antiochos, C. R. DeVore, J. T. Karpen +1

The solar magnetic field is the primary agent that drives solar activity and couples the Sun to the Heliosphere. Although the details of this coupling depend on the quantitative pr…

astro-ph2007★ 216 cited

Generalized Squashing Factors for Covariant Description of Magnetic Connectivity in the Solar Corona

V. S. Titov

The study of magnetic connectivity in the solar corona reveals a need to generalize the field line mapping technique to arbitrary geometry of the boundaries and systems of coordina…

math.ST2007★ 1 cited

Recursive estimation of possibly misspecified MA(1) models: Convergence of a general algorithm

James L. Cantor, David F. Findley

We introduce a recursive algorithm of conveniently general form for estimating the coefficient of a moving average model of order one and obtain convergence results for both correc…

astro-ph2005★ 33 cited

Probing the outer edge of an accretion disk: A Her X-1 turn-on observed with RXTE

M. Kuster, J. Wilms, R. Staubert +4

We present the analysis of Rossi X-ray Timing Explorer (RXTE) observations of the turn-on phase of a 35 day cycle of the X-ray binary Her X-1. During the early phases of the turn-o…