Published in J Chem Phys on October 21, 2007
Milestoning without a Reaction Coordinate. J Chem Theory Comput (2010) 1.47
The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures. J Chem Phys (2010) 1.21
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Steady-state simulations using weighted ensemble path sampling. J Chem Phys (2010) 1.03
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An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates. J Chem Phys (2012) 0.87
Computation of steady-state probability distributions in stochastic models of cellular networks. PLoS Comput Biol (2011) 0.86
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78
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Relation between ordering and shear thinning in colloidal suspensions. Proc Natl Acad Sci U S A (2013) 0.77
Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. J Comput Chem (2015) 0.77
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Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. Protein Sci (2015) 0.77
Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning. J Phys Chem B (2016) 0.77
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Path-sampling strategies for simulating rare events in biomolecular systems. Curr Opin Struct Biol (2016) 0.75
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The immunological synapse balances T cell receptor signaling and degradation. Science (2003) 4.94
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B cell antigen receptor signaling and internalization are mutually exclusive events. PLoS Biol (2006) 1.85
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Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc Natl Acad Sci U S A (2003) 1.46
The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A (2008) 1.39
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Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys (2004) 1.36
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT. Proc Natl Acad Sci U S A (2008) 1.21
A self-reinforcing regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation. Nat Immunol (2012) 1.18
An incoherent regulatory network architecture that orchestrates B cell diversification in response to antigen signaling. Mol Syst Biol (2011) 1.17
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Polymerization of MIP-1 chemokine (CCL3 and CCL4) and clearance of MIP-1 by insulin-degrading enzyme. EMBO J (2010) 1.16
Nonequilibrium umbrella sampling in spaces of many order parameters. J Chem Phys (2009) 1.14
Requirements for contractility in disordered cytoskeletal bundles. New J Phys (2012) 1.12
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Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic Acids Res (2012) 1.06
Signatures of combinatorial regulation in intrinsic biological noise. Proc Natl Acad Sci U S A (2008) 1.05
Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives. Development (2010) 1.02
Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics (2011) 1.02
Delineation of folding pathways of a β-sheet miniprotein. J Phys Chem B (2011) 1.01
Bias annealing: a method for obtaining transition paths de novo. J Chem Phys (2006) 0.96
Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow. Proc Natl Acad Sci U S A (2011) 0.94
Separating forward and backward pathways in nonequilibrium umbrella sampling. J Chem Phys (2009) 0.94
Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophys J (2009) 0.93
A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogeneous environments and under the influence of external fields. J Phys Chem B (2006) 0.92
Enhanced sampling of nonequilibrium steady states. Annu Rev Phys Chem (2010) 0.92
Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol (2012) 0.91
Dynamic coupling between coordinates in a model for biomolecular isomerization. J Chem Phys (2006) 0.91
Mechanistic insights from a quantitative analysis of pollen tube guidance. BMC Plant Biol (2010) 0.89
Orientation-dependent potential of mean force for protein folding. J Chem Phys (2005) 0.86
Distribution of directional change as a signature of complex dynamics. Proc Natl Acad Sci U S A (2013) 0.86
Phase resetting reveals network dynamics underlying a bacterial cell cycle. PLoS Comput Biol (2012) 0.86
A model for TCR gene segment use. J Immunol (2006) 0.85
Model for how retrograde actin flow regulates adhesion traction stresses. J Phys Condens Matter (2010) 0.85
Conformational sampling via a self-regulating effective energy surface. J Chem Phys (2006) 0.84
Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J Phys Chem B (2010) 0.82
Enhancement of diffusion-controlled reaction rates by surface-induced orientational restriction. Biophys J (2005) 0.81
Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: an apparent discrepancy resolved. Biochemistry (2006) 0.81
Apparent directional scanning for DNA repair. Biophys J (2007) 0.80
Steered transition path sampling. J Chem Phys (2012) 0.80
Models of single-molecule experiments with periodic perturbations reveal hidden dynamics in RNA folding. J Phys Chem B (2009) 0.80
Shape dynamics of growing cell walls. Soft Matter (2016) 0.80
How focal adhesion size depends on integrin affinity. Langmuir (2009) 0.79
How noise statistics impact models of enzyme cycles. J Chem Phys (2008) 0.78
Lattice model for self-assembly with application to the formation of cytoskeletal-like structures. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.78
Relation between ordering and shear thinning in colloidal suspensions. Proc Natl Acad Sci U S A (2013) 0.77
Entrainment of a driven oscillator as a dynamical phase transition. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.76
Model for competition from self during passive immunization, with application to broadly neutralizing antibodies for HIV. Vaccine (2011) 0.76
Spreading of colloid clusters in a quasi-one-dimensional channel. J Chem Phys (2010) 0.75
Critical behavior of a model for catalyzed autoamplification. J Chem Phys (2009) 0.75
Structural responses of quasi-two-dimensional colloidal fluids to excitations elicited by nonequilibrium perturbations. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.75
Field theoretic treatment of an effective action for a model of catalyzed autoamplification. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.75
Incorporating friction and collective shear moves into a lattice gas. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.75
Short-time evolution in the adaptive immune system. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.75
Effects of nonproductive binding on the kinetics of enzymatic reactions with patterned substrates. J Chem Phys (2007) 0.75
miR-4728-3p Functions as a Tumor Suppressor in Ulcerative Colitis-associated Colorectal Neoplasia Through Regulation of Focal Adhesion Signaling. Inflamm Bowel Dis (2017) 0.75
Control of genotypic allelic inclusion through TCR surface expression. J Immunol (2005) 0.75
Minimizing memory as an objective for coarse-graining. J Chem Phys (2013) 0.75
How the nature of an observation affects single-trajectory entropies. J Chem Phys (2008) 0.75